pax_global_header 0000666 0000000 0000000 00000000064 14573550650 0014524 g ustar 00root root 0000000 0000000 52 comment=42f8b69799570d73f61bc0d5b6562387d7da4132
bio-0.13.3/ 0000775 0000000 0000000 00000000000 14573550650 0012361 5 ustar 00root root 0000000 0000000 bio-0.13.3/.github/ 0000775 0000000 0000000 00000000000 14573550650 0013721 5 ustar 00root root 0000000 0000000 bio-0.13.3/.github/FUNDING.yml 0000664 0000000 0000000 00000000150 14573550650 0015532 0 ustar 00root root 0000000 0000000 # These are supported funding model platforms
# github: shenwei356
custom: http://paypal.me/shenwei356
bio-0.13.3/.gitignore 0000775 0000000 0000000 00000000424 14573550650 0014354 0 ustar 00root root 0000000 0000000 # Compiled Object files, Static and Dynamic libs (Shared Objects)
*.o
*.a
*.so
# Folders
_obj
_test
# Architecture specific extensions/prefixes
*.[568vq]
[568vq].out
*.cgo1.go
*.cgo2.c
_cgo_defun.c
_cgo_gotypes.go
_cgo_export.*
_testmain.go
*.exe
*.directory
.DS_Store
bio-0.13.3/CHANGELOG.md 0000664 0000000 0000000 00000004330 14573550650 0014172 0 ustar 00root root 0000000 0000000 # Changelog
### v0.13.3 - 2024-03-11
- fix dependency.
### v0.13.2 - 2024-03-11
- seq: increase default value of `seq.ComplementSeqLenThreshold` from 1000 to 1000000, which means only parallelize complement computation for sequences longer than 1Mb.
### v0.13.1 - 2024-02-22
- util: fix computation of L50.
### v0.13.0 - 2024-02-19
- seq: remove the global variable: `seq.ValidateWholeSeq`.
### v0.12.1 - 2024-01-03
- seqio/fai: when using the whole FASTA header as the sequence ID, replace possible tabs in FASTA header with spaces.
### v0.12.0 - 2023-12-04
- seqio/fastx.Reader: reuse the reader with an object pool, this requires users to call reader.Close() after using.
The benefit is that it reduces memory when handling of a lot of sequences.
### v0.11.0 - 2023-12-03
Do not use this version!
- seqio/fastx.Reader: delete reader.Recycle() to avoid API changes.
### v0.10.0 - 2023-12-03
- seqio/fastx.Reader: reuse reader with object pool, this requires users to call reader.Recycle() after using.
### v0.9.3 - 2023-11-11
- seqio/fastx.Reader: fix a panic of nil pointer when some files has file size of 0.
### v0.9.2 - 2023-11-10
- seq/alphabet.IsValid: fix panic: close of closed channel
### v0.9.1 - 2023-11-08
- seqio/fastx.Reader: recycle []byte buffer to save memory for reading a large number of sequences.
### v0.9.0 - 2023-06-25
- util/LengthStats: new method to compute N50 for any number
- seq/alphabet: faster with asciiset
### v0.8.4 - 2023-02-14
- seqio/fai: report error for non-fasta files
### v0.8.3 - 2022-12-02
- util.LengthStats: fix computing Q1 and Q3 for one element.
### v0.8.2 - 2022-11-16
- faidx: allow empty lines at the end of sequences
### v0.8.1 - 2022-09-06
- fastx: fix concurrency bug of `record.FormatToWriter()`.
### v0.8.0 - 2022-09-06
- sketches: added an iterator of SimHash.
### v0.7.1 - 2022-04-19
- taxdump: allow reading empty merged.dmp and delnodes.dmp
### v0.6.4 - 2022-03-13
- update xopen version
### v0.6.3 - 2022-03-12
- use new versin of xopen which support .xz and .zst
### v0.6.2 - 2021-12-01
- taxdump: more robust
### v0.6.1 - 2021-11-16
- taxdump: fix pkg name in errors
### v0.6.0 - 2021-11-08
- move sketches and taxdump packages from unikmer to here
bio-0.13.3/LICENSE 0000775 0000000 0000000 00000002113 14573550650 0013366 0 ustar 00root root 0000000 0000000 Copyright (c) 2013 - 2021 Wei Shen (shenwei356@gmail.com)
The MIT License
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
bio-0.13.3/README.md 0000775 0000000 0000000 00000001266 14573550650 0013650 0 ustar 00root root 0000000 0000000 # bio - a lightweight and high-performance bioinformatics package for Golang
[](https://pkg.go.dev/github.com/shenwei356/bio)
[](https://goreportcard.com/report/github.com/shenwei356/bio)
See sub packages for details.
## Install
go get -u github.com/shenwei356/bio
## Support
Please [open an issue](https://github.com/shenwei356/bio/issues) to report bugs,
propose new functions or ask for help.
## License
Copyright (c) 2013-2021, Wei Shen (shenwei356@gmail.com)
[MIT License](https://github.com/shenwei356/bio/blob/master/LICENSE)
bio-0.13.3/benchmark/ 0000775 0000000 0000000 00000000000 14573550650 0014313 5 ustar 00root root 0000000 0000000 bio-0.13.3/benchmark/fastx/ 0000775 0000000 0000000 00000000000 14573550650 0015440 5 ustar 00root root 0000000 0000000 bio-0.13.3/benchmark/fastx/README.md 0000664 0000000 0000000 00000003641 14573550650 0016723 0 ustar 00root root 0000000 0000000
## FASTA/Q reading and writing
***bio/seqio/fastx has a high performance close to the famous C lib
[`kseq.h`](https://github.com/attractivechaos/klib/blob/master/kseq.h).***
To test the performance, three datasets and their gzip-compressed file are used:
- dataset_A, bacteria genomes, 2.7G
- dataset_B, human genome, 2.9G
- dataset_C, Illumina reads, 2.2G
Summary by [`seqkit`](https://github.com/shenwei356/seqkit):
file seq_format seq_type num_seqs min_len avg_len max_len
dataset_A.fa FASTA DNA 67,748 56 41,442.5 5,976,145
dataset_B.fa FASTA DNA 194 970 15,978,096.5 248,956,422
dataset_C.fq FASTQ DNA 9,186,045 100 100 100
[`seqtk`](https://github.com/lh3/seqtk/)
(Version [1.3-r119-dirty](https://github.com/lh3/seqtk/commit/f6ea81cc30b9232e244dffa94187114275389132),
using `kseq.h`)
and [`seqkit`](https://github.com/shenwei356/seqkit)
(Version [v2.4.0](https://github.com/shenwei356/seqkit/releases/tag/v2.4.0),
using this package) were used to test.
**Note** that `seqtk` does not support wrapped (fixed line width) ouputing, so `seqkit` uses
`-w 0` to disable outputing wrapping.
Script [`memusg`](https://github.com/shenwei356/memusg) is used to assess running time
and peak memory usage.
[Commands](https://github.com/shenwei356/bio/blob/master/benchmark/)
Tests were repeated 4 times and average time and memory usage were computed.
Results:
Notes:
- `seqkit` uses 4 threads by default.
- `seqkit_t1` uses 1 thread.
- `seqtk` is single-threaded.
- `seqtk+gzip`: `seqtk` pipes data to the single-threaded `gzip`.
- `seqtk+pigz`: `seqtk` pipes data to the multithreaded `pigz` which uses 4 threads here.
## Run
./run.pl -n 4 run_benchmark_*.sh --outfile benchmark.tsv
# PLOT
./plot.sh
bio-0.13.3/benchmark/fastx/benchmark.tsv 0000775 0000000 0000000 00000010116 14573550650 0020132 0 ustar 00root root 0000000 0000000 test dataset app time mem
Plain text dataset_A.fa seqkit 2.54 28332
Plain text dataset_A.fa seqkit 2.53 28432
Plain text dataset_A.fa seqkit 2.64 29680
Plain text dataset_A.fa seqkit 2.54 27520
Plain text dataset_A.fa seqkit_t1 3.77 31888
Plain text dataset_A.fa seqkit_t1 3.67 31836
Plain text dataset_A.fa seqkit_t1 3.23 29540
Plain text dataset_A.fa seqkit_t1 3.96 27884
Plain text dataset_A.fa seqtk 2.77 7684
Plain text dataset_A.fa seqtk 2.65 7664
Plain text dataset_A.fa seqtk 2.65 7756
Plain text dataset_A.fa seqtk 2.76 7668
Plain text dataset_B.fa seqkit 3.11 1039000
Plain text dataset_B.fa seqkit 3.11 1035532
Plain text dataset_B.fa seqkit 3.22 1034608
Plain text dataset_B.fa seqkit 3.21 1037848
Plain text dataset_B.fa seqkit_t1 3.23 1037696
Plain text dataset_B.fa seqkit_t1 3.34 1035184
Plain text dataset_B.fa seqkit_t1 3.46 1035184
Plain text dataset_B.fa seqkit_t1 3.35 1038660
Plain text dataset_B.fa seqtk 3.11 244940
Plain text dataset_B.fa seqtk 3.11 244988
Plain text dataset_B.fa seqtk 3.12 244948
Plain text dataset_B.fa seqtk 3.20 244944
Plain text dataset_C.fq seqkit 3.22 24560
Plain text dataset_C.fq seqkit 3.28 24496
Plain text dataset_C.fq seqkit 3.28 14176
Plain text dataset_C.fq seqkit 3.23 14296
Plain text dataset_C.fq seqkit_t1 3.79 14192
Plain text dataset_C.fq seqkit_t1 3.58 24628
Plain text dataset_C.fq seqkit_t1 3.68 14524
Plain text dataset_C.fq seqkit_t1 4.15 14288
Plain text dataset_C.fq seqtk 4.15 1028
Plain text dataset_C.fq seqtk 4.15 1088
Plain text dataset_C.fq seqtk 4.15 1020
Plain text dataset_C.fq seqtk 4.26 1028
Gzip compressed dataset_A.fa.gz seqkit 14.27 57764
Gzip compressed dataset_A.fa.gz seqkit 14.38 58748
Gzip compressed dataset_A.fa.gz seqkit 14.45 55004
Gzip compressed dataset_A.fa.gz seqkit 14.49 57792
Gzip compressed dataset_A.fa.gz seqkit_t1 41.86 42856
Gzip compressed dataset_A.fa.gz seqkit_t1 41.43 43884
Gzip compressed dataset_A.fa.gz seqkit_t1 42.50 41936
Gzip compressed dataset_A.fa.gz seqkit_t1 40.89 44064
Gzip compressed dataset_A.fa.gz seqtk+gzip 461.54 7700
Gzip compressed dataset_A.fa.gz seqtk+gzip 460.74 7820
Gzip compressed dataset_A.fa.gz seqtk+gzip 461.59 7748
Gzip compressed dataset_A.fa.gz seqtk+gzip 459.01 7800
Gzip compressed dataset_A.fa.gz seqtk+pigz 118.43 7748
Gzip compressed dataset_A.fa.gz seqtk+pigz 117.57 7664
Gzip compressed dataset_A.fa.gz seqtk+pigz 120.28 7696
Gzip compressed dataset_A.fa.gz seqtk+pigz 119.26 7724
Gzip compressed dataset_B.fa.gz seqkit 25.37 1045592
Gzip compressed dataset_B.fa.gz seqkit 25.05 1044708
Gzip compressed dataset_B.fa.gz seqkit 25.81 1042072
Gzip compressed dataset_B.fa.gz seqkit 25.46 1045288
Gzip compressed dataset_B.fa.gz seqkit_t1 46.53 1043316
Gzip compressed dataset_B.fa.gz seqkit_t1 46.19 1041472
Gzip compressed dataset_B.fa.gz seqkit_t1 46.30 1041008
Gzip compressed dataset_B.fa.gz seqkit_t1 46.80 1042332
Gzip compressed dataset_B.fa.gz seqtk+gzip 457.71 245104
Gzip compressed dataset_B.fa.gz seqtk+gzip 461.24 245072
Gzip compressed dataset_B.fa.gz seqtk+gzip 463.54 245164
Gzip compressed dataset_B.fa.gz seqtk+gzip 467.39 245208
Gzip compressed dataset_B.fa.gz seqtk+pigz 128.74 245028
Gzip compressed dataset_B.fa.gz seqtk+pigz 126.62 245100
Gzip compressed dataset_B.fa.gz seqtk+pigz 128.22 245076
Gzip compressed dataset_B.fa.gz seqtk+pigz 130.17 245100
Gzip compressed dataset_C.fq.gz seqkit 9.05 40948
Gzip compressed dataset_C.fq.gz seqkit 8.87 41016
Gzip compressed dataset_C.fq.gz seqkit 9.23 38484
Gzip compressed dataset_C.fq.gz seqkit 9.05 39380
Gzip compressed dataset_C.fq.gz seqkit_t1 31.18 30100
Gzip compressed dataset_C.fq.gz seqkit_t1 30.59 29512
Gzip compressed dataset_C.fq.gz seqkit_t1 30.50 29052
Gzip compressed dataset_C.fq.gz seqkit_t1 30.66 29424
Gzip compressed dataset_C.fq.gz seqtk+gzip 188.89 1024
Gzip compressed dataset_C.fq.gz seqtk+gzip 190.83 1080
Gzip compressed dataset_C.fq.gz seqtk+gzip 190.95 964
Gzip compressed dataset_C.fq.gz seqtk+gzip 191.15 968
Gzip compressed dataset_C.fq.gz seqtk+pigz 49.13 1080
Gzip compressed dataset_C.fq.gz seqtk+pigz 48.17 968
Gzip compressed dataset_C.fq.gz seqtk+pigz 48.11 1032
Gzip compressed dataset_C.fq.gz seqtk+pigz 49.28 964
bio-0.13.3/benchmark/fastx/benchmark.tsv.png 0000664 0000000 0000000 00000516350 14573550650 0020725 0 ustar 00root root 0000000 0000000 PNG
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`a+= Q( Q( Q( Q( Q( Q( Q( Q( Q( Q( QIrY IENDB` bio-0.13.3/benchmark/fastx/plot.R 0000775 0000000 0000000 00000011336 14573550650 0016550 0 ustar 00root root 0000000 0000000 #!/usr/bin/env Rscript
library(argparse)
library(ggplot2)
library(dplyr)
library(scales)
library(ggthemes)
library(ggrepel)
parser <-
ArgumentParser(description = "", formatter_class = "argparse.RawTextHelpFormatter")
parser$add_argument("-i", "--infile", type = "character",
help = "result file generated by run.pl")
parser$add_argument("-o", "--outfile", type = "character",
default = "",
help = "result figure file")
parser$add_argument("--width", type = "double",
default = 8,
help = "result file width")
parser$add_argument("--height", type = "double",
default = 6,
help = "result file height")
parser$add_argument("--lx", type = "double",
default = 0.85,
help = "x of legend position")
parser$add_argument("--ly", type = "double",
default = 0.25,
help = "y of legend position")
parser$add_argument("--dpi", type = "integer",
default = 300,
help = "DPI")
parser$add_argument("--labcolor", type = "character",
default = "Datasets",
help = "label of color")
parser$add_argument("--labshape", type = "character",
default = "Tools",
help = "label of shape")
args <- parser$parse_args()
if (is.null(args$infile)) {
write("ERROR: Input file (generated by run.pl) needed!\n", file = stderr())
quit("no", 1)
}
if (args$outfile == "") {
args$outfile = paste(args$infile, ".png", sep = "")
}
w <- args$width
h <- args$height
df <- read.csv(args$infile, sep = "\t")
# sort
df$test <- factor(df$test, levels = unique(df$test), ordered = TRUE)
df$app <- factor(df$app, levels = unique(df$app), ordered = TRUE)
df$dataset <-
factor(df$dataset, levels = unique(df$dataset), ordered = TRUE)
# humanize mem unit
max_mem <- max(df$mem)
unit <- "KB"
if (max_mem > 1024 * 1024) {
df <- df %>% mutate(mem2 = mem / 1024 / 1024)
unit <- "GB"
} else if (max_mem > 1024) {
df <- df %>% mutate(mem2 = mem / 1024)
unit <- "MB"
} else {
df <- df %>% mutate(mem2 = mem / 1)
unit <- "KB"
}
df2 <- df %>%
group_by(test, dataset, app) %>%
summarize(
mem_stdev = sd(mem2) / sqrt(length(mem2)),
mem_mean = mean(mem2),
time_stdev = sd(time) / sqrt(length(time)),
time_mean = mean(time)
)
p <-
ggplot(
df2, aes(
x = mem_mean, y = time_mean,
xmin = mem_mean - mem_stdev,
xmax = mem_mean + mem_stdev,
ymin = time_mean - time_stdev,
ymax = time_mean + time_stdev,
color = dataset,
shape = app,
label = app
)
) +
# geom_hline(aes(yintercept = time_mean, color = app), size = 0.15, alpha = 0.4) +
# geom_vline(aes(xintercept = mem_mean, color = app), size = 0.15, alpha = 0.4) +
geom_point(size = 3.5, alpha = 0.7) +
# geom_text_repel(size = 6, max.iter = 200000, min.segment.length = 0) +
scale_color_wsj() +
facet_grid(test ~ ., scales = "free_y") +
# ylim(0, max(df$time)) +
xlim(0, max(df$mem2)) +
ggtitle(paste("FASTA/Q reading + writing performance")) +
ylab("Time (s)") +
xlab(paste("Peak Memory (", unit, ")", sep = "")) +
labs(color = args$labcolor, shape = args$labshape)
p <- p +
theme_bw() +
theme(
panel.border = element_rect(color = "grey20", size = 0.8),
panel.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
plot.margin = unit(c(0.1,0.4,0.1,0.1),"cm"),
axis.ticks.y = element_line(size = 0.6),
axis.ticks.x = element_line(size = 0.6),
strip.background = element_rect(
colour = "white", fill = "grey95",
size = 0.2
),
strip.text.y = element_text(size = 13),
legend.text = element_text(size = 13),
# legend.position = c(args$lx,args$ly),
legend.position = "right",
legend.background = element_rect(fill = "transparent"),
legend.key.size = unit(0.6, "cm"),
legend.key = element_blank(),
legend.text.align = 0,
legend.box.just = "left",
legend.spacing.y = unit(0.1, "cm"), # space between key and text
text = element_text(
size = 12, family = "arial" #, face = "bold"
),
plot.title = element_text(size = 15)
)
if (grepl("tiff?$", args$outfile, perl = TRUE, ignore.case = TRUE)) {
ggsave(
p, file = args$outfile, width = w, height = h, dpi = args$dpi, compress =
"lzw"
)
} else {
ggsave(
p, file = args$outfile, width = w, height = h, dpi = args$dpi
)
}
# p <- p + scale_color_manual(values = rep("black", length(df$app)))
#
# ggsave(
# p, file = paste("benchmark-", gsub(" ", "-", tolower(test1)), ".grey.png", sep = ""), width = w, height = h
# )
bio-0.13.3/benchmark/fastx/plot.sh 0000775 0000000 0000000 00000000131 14573550650 0016750 0 ustar 00root root 0000000 0000000 #!/bin/sh
./plot.R -i benchmark.tsv --dpi 300 --width 6 --height 6 --lx 0.82 --ly 0.23
bio-0.13.3/benchmark/fastx/plot_old.R 0000775 0000000 0000000 00000012173 14573550650 0017406 0 ustar 00root root 0000000 0000000 #!/usr/bin/env Rscript
library(argparse)
library(ggplot2)
library(dplyr)
library(scales)
library(ggthemes)
library(ggrepel)
parser <-
ArgumentParser(description = "", formatter_class = "argparse.RawTextHelpFormatter")
parser$add_argument("-i", "--infile", type = "character",
help = "result file generated by run.pl")
parser$add_argument("-o", "--outfile", type = "character",
default = "",
help = "result figure file")
parser$add_argument("--width", type = "double",
default = 8,
help = "result file width")
parser$add_argument("--height", type = "double",
default = 6,
help = "result file height")
parser$add_argument("--lx", type = "double",
default = 0.85,
help = "x of legend position")
parser$add_argument("--ly", type = "double",
default = 0.25,
help = "y of legend position")
parser$add_argument("--dpi", type = "integer",
default = 300,
help = "DPI")
parser$add_argument("--labcolor", type = "character",
default = "Tools",
help = "label of color")
parser$add_argument("--labshape", type = "character",
default = "Datasets",
help = "label of shape")
args <- parser$parse_args()
if (is.null(args$infile)) {
write("ERROR: Input file (generated by run.pl) needed!\n", file = stderr())
quit("no", 1)
}
if (args$outfile == "") {
args$outfile = paste(args$infile, ".png", sep = "")
}
w <- args$width
h <- args$height
df <- read.csv(args$infile, sep = "\t")
# sort
df$test <- factor(df$test, levels = unique(df$test), ordered = TRUE)
df$app <- factor(df$app, levels = unique(df$app), ordered = TRUE)
df$dataset <-
factor(df$dataset, levels = unique(df$dataset), ordered = TRUE)
# humanize mem unit
max_mem <- max(df$mem)
unit <- "KB"
if (max_mem > 1024 * 1024) {
df <- df %>% mutate(mem2 = mem / 1024 / 1024)
unit <- "GB"
} else if (max_mem > 1024) {
df <- df %>% mutate(mem2 = mem / 1024)
unit <- "MB"
} else {
df <- df %>% mutate(mem2 = mem / 1)
unit <- "KB"
}
df2 <- df %>%
group_by(test, dataset, app) %>%
summarize(
mem_stdev = sd(mem2) / sqrt(length(mem2)),
mem_mean = mean(mem2),
time_stdev = sd(time) / sqrt(length(time)),
time_mean = mean(time)
)
p <-
ggplot(
df2, aes(
x = mem_mean, y = time_mean,
xmin = mem_mean - mem_stdev,
xmax = mem_mean + mem_stdev,
ymin = time_mean - time_stdev,
ymax = time_mean + time_stdev,
color = app, shape = dataset, label = app
)
) +
geom_hline(aes(yintercept = time_mean, color = app), size = 0.1, alpha = 0.4) +
geom_vline(aes(xintercept = mem_mean, color = app), size = 0.1, alpha = 0.4) +
geom_point(size = 3) +
# geom_errorbar(width = 20, size = 1, alpha = 1) +
# geom_errorbarh(height = 20/max(df$mem2)*max(df$time),
# size = 1, alpha = 1) +
#
# geom_errorbar(aes(ymin = time_mean, ymax = time_mean),
# width = 40, size = 1, alpha = 1) +
# geom_errorbarh(aes(xmin = mem_mean, xmax = mem_mean),
# height = 40/max(df$mem2)*max(df$time),
# size = 1, alpha = 1) +
#
geom_point(data=df, aes(x = mem2, y = time,
xmin=NULL, xmax=NULL,
ymin=NULL, ymax=NULL),
size = 1, alpha = 0.6) +
geom_text_repel(size = 6, max.iter = 200000) +
scale_color_wsj() +
facet_wrap( ~ test) +
ylim(0, max(df$time)) +
xlim(0, max(df$mem2)) +
# ggtitle(paste("FASTA/Q Manipulation Performance\n", test1, sep = "")) +
ylab("Time (s)") +
xlab(paste("Peak Memory (", unit, ")", sep = "")) +
labs(color = args$labcolor, shape = args$labshape)
p <- p +
theme_bw() +
theme(
panel.border = element_rect(color = "black", size = 1.2),
panel.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.ticks.y = element_line(size = 0.8),
axis.ticks.x = element_line(size = 0.8),
strip.background = element_rect(
colour = "white", fill = "white",
size = 0.2
),
legend.text = element_text(size = 14),
legend.position = c(args$lx,args$ly),
legend.background = element_rect(fill = "transparent"),
legend.key.size = unit(0.6, "cm"),
legend.key = element_blank(),
legend.text.align = 0,
legend.box.just = "left",
strip.text.x = element_text(angle = 0, hjust = 0),
text = element_text(
size = 14, family = "arial", face = "bold"
),
plot.title = element_text(size = 15)
)
if (grepl("tiff?$", args$outfile, perl = TRUE, ignore.case = TRUE)) {
ggsave(
p, file = args$outfile, width = w, height = h, dpi = args$dpi, compress =
"lzw"
)
} else {
ggsave(
p, file = args$outfile, width = w, height = h, dpi = args$dpi
)
}
# p <- p + scale_color_manual(values = rep("black", length(df$app)))
#
# ggsave(
# p, file = paste("benchmark-", gsub(" ", "-", tolower(test1)), ".grey.png", sep = ""), width = w, height = h
# )
bio-0.13.3/benchmark/fastx/plot_old.sh 0000775 0000000 0000000 00000000157 14573550650 0017616 0 ustar 00root root 0000000 0000000 #!/bin/sh
./plot2.R -i benchmark.tsv --dpi 100 --width 5 --height 5 --lx 0.75 --ly 0.28 -o benchmark.tsv2.png
bio-0.13.3/benchmark/fastx/run.pl 0000775 0000000 0000000 00000007746 14573550650 0016622 0 ustar 00root root 0000000 0000000 #!/usr/bin/env perl
use strict;
use Getopt::Long;
use File::Basename;
$0 = basename $0;
my $usage = < \$N, 'outfile|o=s' => \$resultfile, "help|h" => \$help, )
or die $usage;
die $usage if scalar @ARGV == 0 or $help;
my @tests = @ARGV;
open my $fh_result, ">", $resultfile or die "failed to write file: $resultfile\n";
my $title_line = "test\tdataset\tapp\ttime\tmem\n";
print $fh_result $title_line;
for my $test (@tests) {
print STDERR "Test: $test\n";
my $stat = {}; # dataset->app->round
my $stat_mem = {};
my $t = ""; # test name
# run $N times
for my $n ( 1 .. $N ) {
print STDERR "Round: $n\n";
my $outfile = "$test.round$n.out";
# unlink $outfile if -e $outfile;
# run
my $cmd = "sh $test 2>&1 | tee $outfile";
my $fail = run($cmd);
die "failed to run:$cmd\n" if $fail;
# stat
my ( $app, $dataset, $time, $mem );
open my $fh, "<", $outfile or die "failed to read file: $outfile\n";
for my $line (<$fh>) {
if ( $t eq "" and $line =~ /Test: (.+)/ ) {
$t = $1;
}
if ( $line =~ /== (.+)/ ) {
$app = $1;
}
if ( $line =~ /data: (.+)/ ) {
$dataset = $1;
}
if ( $line =~ /time: (.+)/ ) {
$time = $1;
if ( not exists $$stat{$dataset}{$app} ) {
$$stat{$dataset}{$app} = [];
}
push @{ $$stat{$dataset}{$app} }, $time;
}
if ( $line =~ /rss: (\d+)/ ) {
$mem = $1;
if ( not exists $$stat_mem{$dataset}{$app} ) {
$$stat_mem{$dataset}{$app} = [];
}
push @{ $$stat_mem{$dataset}{$app} }, $mem;
}
}
close($fh);
}
# benchmark result
my $statfile = "$test.benchmark.tsv";
open my $fh, ">", $statfile or die "failed to write file: $statfile\n";
print "\n=========[ benchmark result ]========\n";
print $title_line;
print $fh $title_line;
for my $dataset ( sort keys %$stat ) {
my $st = $$stat{$dataset};
for my $app ( sort keys %$st ) {
my $times = $$st{$app};
my $mems = $$stat_mem{$dataset}{$app};
# my ( $time_mean, $time_stdev ) = mean_and_stdev($times);
# my ( $mem_mean, $mem_stdev ) = mean_and_stdev($mems);
for my $i (0..@$times-1) {
my ($time, $mem) = ($$times[$i], $$mems[$i]);
my $data_line = sprintf "%s\t%s\t%s\t%.2f\t%d\n",
$t, $dataset, $app, $time, $mem;
printf $data_line;
printf $fh $data_line;
printf $fh_result $data_line;
}
}
}
close($fh);
}
close($fh_result);
sub run {
my ($cmd) = @_;
system($cmd);
if ( $? == -1 ) {
die "[ERROR] fail to run: $cmd. Command ("
. ( split /\s+/, $cmd )[0]
. ") not found\n";
}
elsif ( $? & 127 ) {
printf STDERR "[ERROR] command died with signal %d, %s coredump\n",
( $? & 127 ), ( $? & 128 ) ? 'with' : 'without';
}
else {
# 0, ok
}
return $?;
}
sub mean_and_stdev($) {
my ($list) = @_;
return ( 0, 0 ) if @$list == 0;
my $sum = 0;
$sum += $_ for @$list;
my $sum_square = 0;
$sum_square += $_ * $_ for @$list;
my $mean = $sum / @$list;
my $variance = $sum_square / @$list - $mean * $mean;
my $std = sqrt $variance;
return ( $mean, $std );
}
bio-0.13.3/benchmark/fastx/run_benchmark_01_plain.sh 0000775 0000000 0000000 00000001711 14573550650 0022300 0 ustar 00root root 0000000 0000000 #!/bin/sh
echo Test: Plain text
echo Output sequences of all apps are not wrapped to fixed length.
echo -en "\n============================================\n";
for f in dataset_*.f{a,q}; do
echo read file once with cat
cat $f > /dev/null;
echo -en "\n------------------------------------\n";
echo == seqkit
echo data: $f;
memusg -t -H seqkit seq $f -w 0 > $f.seqkit.fx;
md5sum $f.seqkit.fx;
/bin/rm $f.seqkit.fx;
echo -en "\n------------------------------------\n";
echo == seqkit_t1
echo data: $f;
memusg -t -H seqkit seq $f -w 0 -j 1 > $f.seqkit.fx;
md5sum $f.seqkit.fx;
/bin/rm $f.seqkit.fx;
echo -en "\n------------------------------------\n";
echo == seqtk
echo data: $f;
memusg -t -H seqtk seq $f > $f.seqtk.fx;
md5sum $f.seqtk.fx;
/bin/rm $f.seqtk.fx;
done
bio-0.13.3/benchmark/fastx/run_benchmark_01_plain.sh.benchmark.tsv 0000664 0000000 0000000 00000003046 14573550650 0025044 0 ustar 00root root 0000000 0000000 test dataset app time mem
Plain text dataset_A.fa seqkit 2.54 28332
Plain text dataset_A.fa seqkit 2.53 28432
Plain text dataset_A.fa seqkit 2.64 29680
Plain text dataset_A.fa seqkit 2.54 27520
Plain text dataset_A.fa seqkit_t1 3.77 31888
Plain text dataset_A.fa seqkit_t1 3.67 31836
Plain text dataset_A.fa seqkit_t1 3.23 29540
Plain text dataset_A.fa seqkit_t1 3.96 27884
Plain text dataset_A.fa seqtk 2.77 7684
Plain text dataset_A.fa seqtk 2.65 7664
Plain text dataset_A.fa seqtk 2.65 7756
Plain text dataset_A.fa seqtk 2.76 7668
Plain text dataset_B.fa seqkit 3.11 1039000
Plain text dataset_B.fa seqkit 3.11 1035532
Plain text dataset_B.fa seqkit 3.22 1034608
Plain text dataset_B.fa seqkit 3.21 1037848
Plain text dataset_B.fa seqkit_t1 3.23 1037696
Plain text dataset_B.fa seqkit_t1 3.34 1035184
Plain text dataset_B.fa seqkit_t1 3.46 1035184
Plain text dataset_B.fa seqkit_t1 3.35 1038660
Plain text dataset_B.fa seqtk 3.11 244940
Plain text dataset_B.fa seqtk 3.11 244988
Plain text dataset_B.fa seqtk 3.12 244948
Plain text dataset_B.fa seqtk 3.20 244944
Plain text dataset_C.fq seqkit 3.22 24560
Plain text dataset_C.fq seqkit 3.28 24496
Plain text dataset_C.fq seqkit 3.28 14176
Plain text dataset_C.fq seqkit 3.23 14296
Plain text dataset_C.fq seqkit_t1 3.79 14192
Plain text dataset_C.fq seqkit_t1 3.58 24628
Plain text dataset_C.fq seqkit_t1 3.68 14524
Plain text dataset_C.fq seqkit_t1 4.15 14288
Plain text dataset_C.fq seqtk 4.15 1028
Plain text dataset_C.fq seqtk 4.15 1088
Plain text dataset_C.fq seqtk 4.15 1020
Plain text dataset_C.fq seqtk 4.26 1028
bio-0.13.3/benchmark/fastx/run_benchmark_01_plain.sh.round1.out 0000664 0000000 0000000 00000003175 14573550650 0024320 0 ustar 00root root 0000000 0000000 Test: Plain text
Output sequences of all apps are not wrapped to fixed length.
============================================
read file once with cat
------------------------------------
== seqkit
data: dataset_A.fa
elapsed time: 2.535
peak rss: 28332
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_A.fa
elapsed time: 3.775
peak rss: 31888
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqkit.fx
------------------------------------
== seqtk
data: dataset_A.fa
elapsed time: 2.767
peak rss: 7684
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqtk.fx
read file once with cat
------------------------------------
== seqkit
data: dataset_B.fa
elapsed time: 3.108
peak rss: 1039000
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_B.fa
elapsed time: 3.225
peak rss: 1037696
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqkit.fx
------------------------------------
== seqtk
data: dataset_B.fa
elapsed time: 3.106
peak rss: 244940
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqtk.fx
read file once with cat
------------------------------------
== seqkit
data: dataset_C.fq
elapsed time: 3.216
peak rss: 24560
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_C.fq
elapsed time: 3.795
peak rss: 14192
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqkit.fx
------------------------------------
== seqtk
data: dataset_C.fq
elapsed time: 4.152
peak rss: 1028
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqtk.fx
bio-0.13.3/benchmark/fastx/run_benchmark_01_plain.sh.round2.out 0000664 0000000 0000000 00000003175 14573550650 0024321 0 ustar 00root root 0000000 0000000 Test: Plain text
Output sequences of all apps are not wrapped to fixed length.
============================================
read file once with cat
------------------------------------
== seqkit
data: dataset_A.fa
elapsed time: 2.532
peak rss: 28432
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_A.fa
elapsed time: 3.670
peak rss: 31836
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqkit.fx
------------------------------------
== seqtk
data: dataset_A.fa
elapsed time: 2.654
peak rss: 7664
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqtk.fx
read file once with cat
------------------------------------
== seqkit
data: dataset_B.fa
elapsed time: 3.114
peak rss: 1035532
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_B.fa
elapsed time: 3.339
peak rss: 1035184
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqkit.fx
------------------------------------
== seqtk
data: dataset_B.fa
elapsed time: 3.114
peak rss: 244988
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqtk.fx
read file once with cat
------------------------------------
== seqkit
data: dataset_C.fq
elapsed time: 3.278
peak rss: 24496
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_C.fq
elapsed time: 3.578
peak rss: 24628
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqkit.fx
------------------------------------
== seqtk
data: dataset_C.fq
elapsed time: 4.150
peak rss: 1088
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqtk.fx
bio-0.13.3/benchmark/fastx/run_benchmark_01_plain.sh.round3.out 0000664 0000000 0000000 00000003175 14573550650 0024322 0 ustar 00root root 0000000 0000000 Test: Plain text
Output sequences of all apps are not wrapped to fixed length.
============================================
read file once with cat
------------------------------------
== seqkit
data: dataset_A.fa
elapsed time: 2.637
peak rss: 29680
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_A.fa
elapsed time: 3.226
peak rss: 29540
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqkit.fx
------------------------------------
== seqtk
data: dataset_A.fa
elapsed time: 2.647
peak rss: 7756
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqtk.fx
read file once with cat
------------------------------------
== seqkit
data: dataset_B.fa
elapsed time: 3.218
peak rss: 1034608
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_B.fa
elapsed time: 3.459
peak rss: 1035184
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqkit.fx
------------------------------------
== seqtk
data: dataset_B.fa
elapsed time: 3.123
peak rss: 244948
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqtk.fx
read file once with cat
------------------------------------
== seqkit
data: dataset_C.fq
elapsed time: 3.283
peak rss: 14176
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_C.fq
elapsed time: 3.679
peak rss: 14524
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqkit.fx
------------------------------------
== seqtk
data: dataset_C.fq
elapsed time: 4.151
peak rss: 1020
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqtk.fx
bio-0.13.3/benchmark/fastx/run_benchmark_01_plain.sh.round4.out 0000664 0000000 0000000 00000003175 14573550650 0024323 0 ustar 00root root 0000000 0000000 Test: Plain text
Output sequences of all apps are not wrapped to fixed length.
============================================
read file once with cat
------------------------------------
== seqkit
data: dataset_A.fa
elapsed time: 2.540
peak rss: 27520
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_A.fa
elapsed time: 3.961
peak rss: 27884
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqkit.fx
------------------------------------
== seqtk
data: dataset_A.fa
elapsed time: 2.764
peak rss: 7668
3eac76c3c6a1e6591f04ff7bd44bbb32 dataset_A.fa.seqtk.fx
read file once with cat
------------------------------------
== seqkit
data: dataset_B.fa
elapsed time: 3.209
peak rss: 1037848
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_B.fa
elapsed time: 3.347
peak rss: 1038660
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqkit.fx
------------------------------------
== seqtk
data: dataset_B.fa
elapsed time: 3.200
peak rss: 244944
af9e765363ffe03aaaaa0a23509f7b32 dataset_B.fa.seqtk.fx
read file once with cat
------------------------------------
== seqkit
data: dataset_C.fq
elapsed time: 3.226
peak rss: 14296
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqkit.fx
------------------------------------
== seqkit_t1
data: dataset_C.fq
elapsed time: 4.152
peak rss: 14288
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqkit.fx
------------------------------------
== seqtk
data: dataset_C.fq
elapsed time: 4.259
peak rss: 1028
f01c87fd0f852d6ec378fab0d58952ad dataset_C.fq.seqtk.fx
bio-0.13.3/benchmark/fastx/run_benchmark_02_gzip.sh 0000775 0000000 0000000 00000002403 14573550650 0022146 0 ustar 00root root 0000000 0000000 #!/bin/sh
echo Test: Gzip compressed
echo Output sequences of all apps are not wrapped to fixed length.
echo -en "\n============================================\n";
for f in dataset_*.f{a,q}.gz; do
echo read file once with cat
cat $f > /dev/null;
echo -en "\n------------------------------------\n";
echo == seqkit
echo data: $f;
memusg -t -H seqkit seq $f -w 0 -o $f.seqkit.gz --compress-level 6;
pigz -cd $f.seqkit.gz | md5sum;
/bin/rm $f.seqkit.gz;
echo -en "\n------------------------------------\n";
echo == seqkit_t1
echo data: $f;
memusg -t -H seqkit seq $f -w 0 -j 1 -o $f.seqkit.gz --compress-level 6;
pigz -cd $f.seqkit.gz | md5sum;
/bin/rm $f.seqkit.gz;
echo -en "\n------------------------------------\n";
echo == seqtk+gzip
echo data: $f;
memusg -t -H seqtk seq $f | gzip -c > $f.seqtk.gz;
pigz -cd $f.seqtk.gz | md5sum
/bin/rm $f.seqtk.gz;
echo -en "\n------------------------------------\n";
echo == seqtk+pigz
echo data: $f;
memusg -t -H seqtk seq $f | pigz -p 4 -c > $f.seqtk.gz;
pigz -cd $f.seqtk.gz | md5sum
/bin/rm $f.seqtk.gz;
done
bio-0.13.3/benchmark/fastx/run_benchmark_02_gzip.sh.benchmark.tsv 0000664 0000000 0000000 00000005102 14573550650 0024706 0 ustar 00root root 0000000 0000000 test dataset app time mem
Gzip compressed dataset_A.fa.gz seqkit 14.27 57764
Gzip compressed dataset_A.fa.gz seqkit 14.38 58748
Gzip compressed dataset_A.fa.gz seqkit 14.45 55004
Gzip compressed dataset_A.fa.gz seqkit 14.49 57792
Gzip compressed dataset_A.fa.gz seqkit_t1 41.86 42856
Gzip compressed dataset_A.fa.gz seqkit_t1 41.43 43884
Gzip compressed dataset_A.fa.gz seqkit_t1 42.50 41936
Gzip compressed dataset_A.fa.gz seqkit_t1 40.89 44064
Gzip compressed dataset_A.fa.gz seqtk+gzip 461.54 7700
Gzip compressed dataset_A.fa.gz seqtk+gzip 460.74 7820
Gzip compressed dataset_A.fa.gz seqtk+gzip 461.59 7748
Gzip compressed dataset_A.fa.gz seqtk+gzip 459.01 7800
Gzip compressed dataset_A.fa.gz seqtk+pigz 118.43 7748
Gzip compressed dataset_A.fa.gz seqtk+pigz 117.57 7664
Gzip compressed dataset_A.fa.gz seqtk+pigz 120.28 7696
Gzip compressed dataset_A.fa.gz seqtk+pigz 119.26 7724
Gzip compressed dataset_B.fa.gz seqkit 25.37 1045592
Gzip compressed dataset_B.fa.gz seqkit 25.05 1044708
Gzip compressed dataset_B.fa.gz seqkit 25.81 1042072
Gzip compressed dataset_B.fa.gz seqkit 25.46 1045288
Gzip compressed dataset_B.fa.gz seqkit_t1 46.53 1043316
Gzip compressed dataset_B.fa.gz seqkit_t1 46.19 1041472
Gzip compressed dataset_B.fa.gz seqkit_t1 46.30 1041008
Gzip compressed dataset_B.fa.gz seqkit_t1 46.80 1042332
Gzip compressed dataset_B.fa.gz seqtk+gzip 457.71 245104
Gzip compressed dataset_B.fa.gz seqtk+gzip 461.24 245072
Gzip compressed dataset_B.fa.gz seqtk+gzip 463.54 245164
Gzip compressed dataset_B.fa.gz seqtk+gzip 467.39 245208
Gzip compressed dataset_B.fa.gz seqtk+pigz 128.74 245028
Gzip compressed dataset_B.fa.gz seqtk+pigz 126.62 245100
Gzip compressed dataset_B.fa.gz seqtk+pigz 128.22 245076
Gzip compressed dataset_B.fa.gz seqtk+pigz 130.17 245100
Gzip compressed dataset_C.fq.gz seqkit 9.05 40948
Gzip compressed dataset_C.fq.gz seqkit 8.87 41016
Gzip compressed dataset_C.fq.gz seqkit 9.23 38484
Gzip compressed dataset_C.fq.gz seqkit 9.05 39380
Gzip compressed dataset_C.fq.gz seqkit_t1 31.18 30100
Gzip compressed dataset_C.fq.gz seqkit_t1 30.59 29512
Gzip compressed dataset_C.fq.gz seqkit_t1 30.50 29052
Gzip compressed dataset_C.fq.gz seqkit_t1 30.66 29424
Gzip compressed dataset_C.fq.gz seqtk+gzip 188.89 1024
Gzip compressed dataset_C.fq.gz seqtk+gzip 190.83 1080
Gzip compressed dataset_C.fq.gz seqtk+gzip 190.95 964
Gzip compressed dataset_C.fq.gz seqtk+gzip 191.15 968
Gzip compressed dataset_C.fq.gz seqtk+pigz 49.13 1080
Gzip compressed dataset_C.fq.gz seqtk+pigz 48.17 968
Gzip compressed dataset_C.fq.gz seqtk+pigz 48.11 1032
Gzip compressed dataset_C.fq.gz seqtk+pigz 49.28 964
bio-0.13.3/benchmark/fastx/run_benchmark_02_gzip.sh.round1.out 0000664 0000000 0000000 00000003675 14573550650 0024174 0 ustar 00root root 0000000 0000000 Test: Gzip compressed
Output sequences of all apps are not wrapped to fixed length.
============================================
read file once with cat
------------------------------------
== seqkit
data: dataset_A.fa.gz
elapsed time: 14.269
peak rss: 57764
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqkit_t1
data: dataset_A.fa.gz
elapsed time: 41.863
peak rss: 42856
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqtk+gzip
data: dataset_A.fa.gz
elapsed time: 461.541
peak rss: 7700
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqtk+pigz
data: dataset_A.fa.gz
elapsed time: 118.433
peak rss: 7748
3eac76c3c6a1e6591f04ff7bd44bbb32 -
read file once with cat
------------------------------------
== seqkit
data: dataset_B.fa.gz
elapsed time: 25.374
peak rss: 1045592
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqkit_t1
data: dataset_B.fa.gz
elapsed time: 46.531
peak rss: 1043316
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqtk+gzip
data: dataset_B.fa.gz
elapsed time: 457.706
peak rss: 245104
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqtk+pigz
data: dataset_B.fa.gz
elapsed time: 128.742
peak rss: 245028
af9e765363ffe03aaaaa0a23509f7b32 -
read file once with cat
------------------------------------
== seqkit
data: dataset_C.fq.gz
elapsed time: 9.047
peak rss: 40948
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqkit_t1
data: dataset_C.fq.gz
elapsed time: 31.182
peak rss: 30100
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqtk+gzip
data: dataset_C.fq.gz
elapsed time: 188.893
peak rss: 1024
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqtk+pigz
data: dataset_C.fq.gz
elapsed time: 49.132
peak rss: 1080
f01c87fd0f852d6ec378fab0d58952ad -
bio-0.13.3/benchmark/fastx/run_benchmark_02_gzip.sh.round2.out 0000664 0000000 0000000 00000003674 14573550650 0024174 0 ustar 00root root 0000000 0000000 Test: Gzip compressed
Output sequences of all apps are not wrapped to fixed length.
============================================
read file once with cat
------------------------------------
== seqkit
data: dataset_A.fa.gz
elapsed time: 14.379
peak rss: 58748
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqkit_t1
data: dataset_A.fa.gz
elapsed time: 41.432
peak rss: 43884
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqtk+gzip
data: dataset_A.fa.gz
elapsed time: 460.744
peak rss: 7820
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqtk+pigz
data: dataset_A.fa.gz
elapsed time: 117.571
peak rss: 7664
3eac76c3c6a1e6591f04ff7bd44bbb32 -
read file once with cat
------------------------------------
== seqkit
data: dataset_B.fa.gz
elapsed time: 25.051
peak rss: 1044708
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqkit_t1
data: dataset_B.fa.gz
elapsed time: 46.188
peak rss: 1041472
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqtk+gzip
data: dataset_B.fa.gz
elapsed time: 461.238
peak rss: 245072
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqtk+pigz
data: dataset_B.fa.gz
elapsed time: 126.616
peak rss: 245100
af9e765363ffe03aaaaa0a23509f7b32 -
read file once with cat
------------------------------------
== seqkit
data: dataset_C.fq.gz
elapsed time: 8.866
peak rss: 41016
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqkit_t1
data: dataset_C.fq.gz
elapsed time: 30.589
peak rss: 29512
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqtk+gzip
data: dataset_C.fq.gz
elapsed time: 190.831
peak rss: 1080
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqtk+pigz
data: dataset_C.fq.gz
elapsed time: 48.170
peak rss: 968
f01c87fd0f852d6ec378fab0d58952ad -
bio-0.13.3/benchmark/fastx/run_benchmark_02_gzip.sh.round3.out 0000664 0000000 0000000 00000003674 14573550650 0024175 0 ustar 00root root 0000000 0000000 Test: Gzip compressed
Output sequences of all apps are not wrapped to fixed length.
============================================
read file once with cat
------------------------------------
== seqkit
data: dataset_A.fa.gz
elapsed time: 14.449
peak rss: 55004
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqkit_t1
data: dataset_A.fa.gz
elapsed time: 42.497
peak rss: 41936
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqtk+gzip
data: dataset_A.fa.gz
elapsed time: 461.587
peak rss: 7748
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqtk+pigz
data: dataset_A.fa.gz
elapsed time: 120.277
peak rss: 7696
3eac76c3c6a1e6591f04ff7bd44bbb32 -
read file once with cat
------------------------------------
== seqkit
data: dataset_B.fa.gz
elapsed time: 25.806
peak rss: 1042072
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqkit_t1
data: dataset_B.fa.gz
elapsed time: 46.299
peak rss: 1041008
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqtk+gzip
data: dataset_B.fa.gz
elapsed time: 463.542
peak rss: 245164
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqtk+pigz
data: dataset_B.fa.gz
elapsed time: 128.218
peak rss: 245076
af9e765363ffe03aaaaa0a23509f7b32 -
read file once with cat
------------------------------------
== seqkit
data: dataset_C.fq.gz
elapsed time: 9.227
peak rss: 38484
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqkit_t1
data: dataset_C.fq.gz
elapsed time: 30.496
peak rss: 29052
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqtk+gzip
data: dataset_C.fq.gz
elapsed time: 190.946
peak rss: 964
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqtk+pigz
data: dataset_C.fq.gz
elapsed time: 48.109
peak rss: 1032
f01c87fd0f852d6ec378fab0d58952ad -
bio-0.13.3/benchmark/fastx/run_benchmark_02_gzip.sh.round4.out 0000664 0000000 0000000 00000003673 14573550650 0024175 0 ustar 00root root 0000000 0000000 Test: Gzip compressed
Output sequences of all apps are not wrapped to fixed length.
============================================
read file once with cat
------------------------------------
== seqkit
data: dataset_A.fa.gz
elapsed time: 14.493
peak rss: 57792
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqkit_t1
data: dataset_A.fa.gz
elapsed time: 40.889
peak rss: 44064
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqtk+gzip
data: dataset_A.fa.gz
elapsed time: 459.014
peak rss: 7800
3eac76c3c6a1e6591f04ff7bd44bbb32 -
------------------------------------
== seqtk+pigz
data: dataset_A.fa.gz
elapsed time: 119.257
peak rss: 7724
3eac76c3c6a1e6591f04ff7bd44bbb32 -
read file once with cat
------------------------------------
== seqkit
data: dataset_B.fa.gz
elapsed time: 25.457
peak rss: 1045288
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqkit_t1
data: dataset_B.fa.gz
elapsed time: 46.805
peak rss: 1042332
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqtk+gzip
data: dataset_B.fa.gz
elapsed time: 467.395
peak rss: 245208
af9e765363ffe03aaaaa0a23509f7b32 -
------------------------------------
== seqtk+pigz
data: dataset_B.fa.gz
elapsed time: 130.173
peak rss: 245100
af9e765363ffe03aaaaa0a23509f7b32 -
read file once with cat
------------------------------------
== seqkit
data: dataset_C.fq.gz
elapsed time: 9.055
peak rss: 39380
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqkit_t1
data: dataset_C.fq.gz
elapsed time: 30.655
peak rss: 29424
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqtk+gzip
data: dataset_C.fq.gz
elapsed time: 191.151
peak rss: 968
f01c87fd0f852d6ec378fab0d58952ad -
------------------------------------
== seqtk+pigz
data: dataset_C.fq.gz
elapsed time: 49.281
peak rss: 964
f01c87fd0f852d6ec378fab0d58952ad -
bio-0.13.3/featio/ 0000775 0000000 0000000 00000000000 14573550650 0013630 5 ustar 00root root 0000000 0000000 bio-0.13.3/featio/_bed/ 0000775 0000000 0000000 00000000000 14573550650 0014521 5 ustar 00root root 0000000 0000000 bio-0.13.3/featio/_bed/bed.go 0000664 0000000 0000000 00000023540 14573550650 0015606 0 ustar 00root root 0000000 0000000 //Package bed is used to read bed features.
// ref: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
// ref: https://github.com/biogo/biogo/blob/master/io/featio/bed/bed.go
package bed
import (
"errors"
"fmt"
"os"
"reflect"
"regexp"
"runtime"
"strconv"
"strings"
"github.com/shenwei356/breader"
)
var (
// ErrBadBEDType error
ErrBadBEDType = errors.New("bad BED type")
// ErrBadBrowserLine error
ErrBadBrowserLine = errors.New("bad browser line")
)
// Feature is the interface of BED feature
type Feature interface {
Chr() string
Start() int
End() int
Len() int
Strand() *string
String() string
}
// BED3 struct
type BED3 struct {
Chrom string
ChromStart int
ChromEnd int
}
// Chr returns chromosome
func (b *BED3) Chr() string { return b.Chrom }
// Start returns start
func (b *BED3) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED3) End() int { return b.ChromEnd }
// Length returns length
func (b *BED3) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED3) Strand() *string { return nil }
// Name returns name
func (b *BED3) Name() string { return b.String() }
func (b *BED3) String() string {
return fmt.Sprintf("BED3 %s:[%d,%d)", b.Chrom, b.ChromStart, b.ChromEnd)
}
func parseBED3(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 3 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
return BED3{items[0], start, end}, true, nil
}
// BED4 struct
type BED4 struct {
Chrom string
ChromStart int
ChromEnd int
FeatName string
}
// Chr returns chromosome
func (b *BED4) Chr() string { return b.Chrom }
// Start returns start
func (b *BED4) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED4) End() int { return b.ChromEnd }
// Length returns length
func (b *BED4) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED4) Strand() *string { return nil }
// Name returns name
func (b *BED4) Name() string { return b.FeatName }
func (b *BED4) String() string {
return fmt.Sprintf("BED4 %s:[%d,%d) %s", b.Chrom, b.ChromStart, b.ChromEnd, b.FeatName)
}
func parseBED4(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 4 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
return BED4{items[0], start, end, items[3]}, true, nil
}
// BED5 struct
type BED5 struct {
Chrom string
ChromStart int
ChromEnd int
FeatName string
FeatScore int
}
// Chr returns chromosome
func (b *BED5) Chr() string { return b.Chrom }
// Start returns start
func (b *BED5) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED5) End() int { return b.ChromEnd }
// Length returns length
func (b *BED5) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED5) Strand() *string { return nil }
// Name returns name
func (b *BED5) Name() string { return b.FeatName }
func (b *BED5) String() string {
return fmt.Sprintf("BED5 %s:[%d,%d) %s (score: %d)", b.Chrom, b.ChromStart, b.ChromEnd, b.FeatName, b.FeatScore)
}
func parseBED5(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 5 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
score, err := strconv.Atoi(items[4])
if err != nil {
return nil, false, fmt.Errorf("bad score: %s", items[4])
}
return BED5{items[0], start, end, items[3], score}, true, nil
}
// BED6 struct
type BED6 struct {
Chrom string
ChromStart int
ChromEnd int
FeatName string
FeatScore int
FeatStrand *string
}
// Chr returns chromosome
func (b *BED6) Chr() string { return b.Chrom }
// Start returns start
func (b *BED6) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED6) End() int { return b.ChromEnd }
// Length returns length
func (b *BED6) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED6) Strand() *string { return b.FeatStrand }
// Name returns name
func (b *BED6) Name() string { return b.FeatName }
func (b *BED6) String() string {
return fmt.Sprintf("BED6 %s:[%d,%d)%s %s (score: %d)", b.Chrom, b.ChromStart, b.ChromEnd, *b.FeatStrand, b.FeatName, b.FeatScore)
}
func parseBED6(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 6 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
score, err := strconv.Atoi(items[4])
if err != nil {
return nil, false, fmt.Errorf("bad score: %s", items[4])
}
var strand *string
if items[5] != "." {
strand = &items[5]
}
return BED6{items[0], start, end, items[3], score, strand}, true, nil
}
// BED12 struct
type BED12 struct {
Chrom string
ChromStart int
ChromEnd int
FeatName string
FeatScore int
FeatStrand *string
ThickStart int
ThickEnd int
RGB string
BlockCount int
BlockSizes []int
BlockStarts []int
}
// Chr returns chromosome
func (b *BED12) Chr() string { return b.Chrom }
// Start returns start
func (b *BED12) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED12) End() int { return b.ChromEnd }
// Length returns length
func (b *BED12) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED12) Strand() *string { return b.FeatStrand }
// Name returns name
func (b *BED12) Name() string { return b.FeatName }
func (b *BED12) String() string {
return fmt.Sprintf("BED12 %s:[%d,%d)%s %s (score: %d)", b.Chrom, b.ChromStart, b.ChromEnd, *b.FeatStrand, b.FeatName, b.FeatScore)
}
func parseBED12(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 12 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
score, err := strconv.Atoi(items[4])
if err != nil {
return nil, false, fmt.Errorf("bad score: %s", items[4])
}
var strand *string
if items[5] != "." {
strand = &items[5]
}
thickStart, err := strconv.Atoi(items[6])
if err != nil {
return nil, false, fmt.Errorf("bad thick start: %s", items[6])
}
thickEnd, err := strconv.Atoi(items[7])
if err != nil {
return nil, false, fmt.Errorf("bad thick end: %s", items[7])
}
blockCount, err := strconv.Atoi(items[9])
if err != nil {
return nil, false, fmt.Errorf("bad block count: %s", items[9])
}
blockSizes := []int{}
if blockCount > 0 {
items2 := strings.Split(items[10], ",")
for _, size := range items2[0:blockCount] {
s, err := strconv.Atoi(size)
if err != nil {
return nil, false, fmt.Errorf("bad block size: %s", size)
}
blockSizes = append(blockSizes, s)
}
}
blockStarts := []int{}
if blockCount > 0 {
items2 := strings.Split(items[11], ",")
for _, start := range items2[0:blockCount] {
s, err := strconv.Atoi(start)
if err != nil {
return nil, false, fmt.Errorf("bad block start: %s", start)
}
blockStarts = append(blockStarts, s)
}
}
return BED12{items[0], start, end, items[3], score, strand,
thickStart, thickEnd, items[8], blockCount, blockSizes, blockStarts}, true, nil
}
type meta struct {
name string
details map[string]string
}
// TrackItemRegexp is regular expression for parsing track items
var TrackItemRegexp = regexp.MustCompile(`(\w+)="?[^#]+?"?`)
// ReadFeatures returns bed data of a file, availabe type values are 3,4,5,6
func ReadFeatures(file string, n int) ([]Feature, map[string]map[string]string, error) {
if _, err := os.Stat(file); os.IsNotExist(err) {
return nil, nil, err
}
fn := func(line string) (interface{}, bool, error) {
if line[0] == '#' {
return nil, false, nil
}
if string(line[0:7]) == "browser" {
items := strings.Split(strings.TrimRight(line, "\n"), " ")
if len(items) < 3 {
return nil, false, ErrBadBrowserLine
}
details := make(map[string]string)
details[items[1]] = items[2]
return meta{"browser", details}, true, nil
}
if string(line[0:5]) == "track" {
details := make(map[string]string)
found := TrackItemRegexp.FindAllStringSubmatch(line, -1)
for _, sub := range found {
details[sub[0]] = sub[1]
}
return meta{"track", details}, true, nil
}
return nil, false, nil
}
reader, err := breader.NewBufferedReader(file, runtime.NumCPU(), 100, fn)
if err != nil {
return nil, nil, err
}
features := []Feature{}
for chunk := range reader.Ch {
if chunk.Err != nil {
return nil, nil, chunk.Err
}
for _, data := range chunk.Data {
fmt.Println(reflect.TypeOf(data).Kind())
}
}
return features, nil, nil
}
bio-0.13.3/featio/gtf/ 0000775 0000000 0000000 00000000000 14573550650 0014410 5 ustar 00root root 0000000 0000000 bio-0.13.3/featio/gtf/gtf.go 0000664 0000000 0000000 00000010751 14573550650 0015523 0 ustar 00root root 0000000 0000000 // Package gtf is used to read gtf features.
// ref: http://mblab.wustl.edu/GTF22.html
package gtf
import (
"fmt"
"os"
"runtime"
"strconv"
"strings"
"github.com/shenwei356/breader"
)
// Version is the GTF version
const Version = 2.2
var strandPositive = "+"
var strandNegative = "-"
var strandNotspecified = "."
// Feature is the gff feature struct
type Feature struct {
SeqName string
Source string
Feature string
Start int
End int
Score *float64
Strand *string
Frame *int
Attributes []Attribute
}
// Attribute is the attribute
type Attribute struct {
Tag, Value string
}
// Threads for bread.NewBufferedReader()
var Threads = runtime.NumCPU()
// ReadFeatures returns gtf features of a file
func ReadFeatures(file string) ([]Feature, error) {
return ReadFilteredFeatures(file, []string{}, []string{}, []string{})
}
// ReadFilteredFeatures returns gtf features of specific chrs in a file
func ReadFilteredFeatures(file string, chrs []string, feats []string, attrs []string) ([]Feature, error) {
if _, err := os.Stat(file); os.IsNotExist(err) {
return nil, err
}
chrsMap := make(map[string]struct{}, len(chrs))
for _, chr := range chrs {
chrsMap[strings.ToLower(chr)] = struct{}{}
}
featsMap := make(map[string]struct{}, len(feats))
for _, f := range feats {
featsMap[strings.ToLower(f)] = struct{}{}
}
attrsMap := make(map[string]struct{}, len(attrs))
for _, f := range attrs {
attrsMap[strings.ToLower(f)] = struct{}{}
}
fn := func(line string) (interface{}, bool, error) {
if len(line) == 0 || line[0] == '#' {
return nil, false, nil
}
line = strings.TrimRight(line, "\r\n")
items := strings.Split(line, "\t")
if len(items) != 9 {
return nil, false, nil
}
if len(chrs) > 0 { // selected chrs
if _, ok := chrsMap[strings.ToLower(items[0])]; !ok {
return nil, false, nil
}
}
if len(feats) > 0 { // selected features
if _, ok := featsMap[strings.ToLower(items[2])]; !ok {
return nil, false, nil
}
}
var err error
start, err := strconv.Atoi(items[3])
if err != nil {
return nil, false, fmt.Errorf("%s: bad start: %s", items[0], items[3])
}
end, err := strconv.Atoi(items[4])
if err != nil {
return nil, false, fmt.Errorf("%s: bad end: %s", items[0], items[4])
}
// if start > end {
// return nil, false, fmt.Errorf("%s: start (%d) must be < end (%d)", items[0], start, end)
// }
var score *float64
if items[5] != "." {
s, err := strconv.ParseFloat(items[5], 64)
if err != nil {
return nil, false, fmt.Errorf("%s: bad score: %s", items[0], items[5])
}
score = &s
}
var strand *string
if items[6] != "." {
s := items[6]
if s == "+" {
strand = &strandPositive
} else if s == "-" {
strand = &strandNegative
} else {
return nil, false, fmt.Errorf("%s: illegal strand: %s", items[0], s)
}
strand = &s
if start > end {
if s == "+" {
return nil, false, fmt.Errorf(`%s: start (%d) should be < end (%d) when the strand is "+"`, items[0], start, end)
} else {
strand = &strandNegative
tmp := start
start = end
end = tmp
}
}
} else {
strand = &strandNotspecified
}
var frame *int
if items[7] != "." {
f, err := strconv.Atoi(items[7])
if err != nil {
return nil, false, fmt.Errorf("%s: bad frame: %s", items[0], items[7])
}
if !(f == 0 || f == 1 || f == 2) {
return nil, false, fmt.Errorf("%s: illegal frame: %d", items[0], f)
}
frame = &f
}
feature := Feature{items[0], items[1], items[2], start, end, score, strand, frame, nil}
tagValues := strings.Split(items[8], "; ")
if len(tagValues) > 0 {
var ok bool
feature.Attributes = []Attribute{}
for _, tagValue := range tagValues[0 : len(tagValues)-1] {
items2 := strings.SplitN(tagValue, " ", 2)
tag := items2[0]
if _, ok = attrsMap[tag]; !ok {
continue
}
value := items2[1]
// if value[len(value)-1] == ';' {
// value = value[0 : len(value)-1]
// }
if len(value) > 2 {
value = value[1 : len(value)-1]
} else {
value = ""
}
feature.Attributes = append(feature.Attributes, Attribute{tag, value})
}
}
return feature, true, nil
}
reader, err := breader.NewBufferedReader(file, Threads, 100, fn)
if err != nil {
return nil, err
}
features := []Feature{}
for chunk := range reader.Ch {
if chunk.Err != nil {
return nil, chunk.Err
}
for _, data := range chunk.Data {
features = append(features, data.(Feature))
}
}
return features, nil
}
bio-0.13.3/featio/gtf/gtf_test.go 0000664 0000000 0000000 00000001426 14573550650 0016561 0 ustar 00root root 0000000 0000000 package gtf
import (
"fmt"
"testing"
)
func TestGTF(t *testing.T) {
file := "test1.gtf"
features, err := ReadFeatures(file)
if err != nil {
t.Error(err)
return
}
if len(features) != 14 {
t.Error(err)
return
}
for _, feature := range features {
fmt.Println(feature)
}
}
func TestGTF2(t *testing.T) {
file := "test2.gtf"
features, err := ReadFeatures(file)
if err != nil {
t.Error(err)
return
}
if len(features) != 10 {
t.Error(err)
return
}
for _, feature := range features {
fmt.Println(feature)
}
}
func TestGTF3(t *testing.T) {
file := "test3.gtf"
features, err := ReadFeatures(file)
if err != nil {
t.Error(err)
return
}
if len(features) != 6 {
t.Error(err)
return
}
for _, feature := range features {
fmt.Println(feature)
}
}
bio-0.13.3/featio/gtf/test1.gtf 0000664 0000000 0000000 00000002162 14573550650 0016153 0 ustar 00root root 0000000 0000000 140 Twinscan inter 5141 8522 . - . gene_id ""; transcript_id "";
140 Twinscan inter_CNS 8523 9711 . - . gene_id ""; transcript_id "";
140 Twinscan inter 9712 13182 . - . gene_id ""; transcript_id "";
140 Twinscan 3UTR 65149 65487 . - . gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan 3UTR 66823 66992 . - . gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan stop_codon 66993 66995 . - 0 gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan CDS 66996 66999 . - 1 gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan intron_CNS 70103 70151 . - . gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan CDS 70207 70294 . - 2 gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan CDS 71696 71807 . - 0 gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan start_codon 71805 71806 . - 0 gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan start_codon 73222 73222 . - 2 gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan CDS 73222 73222 . - 0 gene_id "140.000"; transcript_id "140.000.1";
140 Twinscan 5UTR 73223 73504 . - . gene_id "140.000"; transcript_id "140.000.1";
bio-0.13.3/featio/gtf/test2.gtf 0000664 0000000 0000000 00000001441 14573550650 0016153 0 ustar 00root root 0000000 0000000 381 Twinscan exon 150 200 . + . gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan exon 300 401 . + . gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan CDS 380 401 . + 0 gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan exon 501 650 . + . gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan CDS 501 650 . + 2 gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan exon 700 800 . + . gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan CDS 700 707 . + 2 gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan exon 900 1000 . + . gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan start_codon 380 382 . + 0 gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan stop_codon 708 710 . + 0 gene_id "381.000"; transcript_id "381.000.1";
bio-0.13.3/featio/gtf/test3.gtf 0000664 0000000 0000000 00000001770 14573550650 0016161 0 ustar 00root root 0000000 0000000 NC_002516.2 genbank gene 6261828 6263564 . - 0 gene_id ""; transcript_id ""; db_xref "GeneID:878127"; product "";
NC_002516.2 genbank CDS 6261828 6263564 . - 0 gene_id ""; transcript_id ""; protein_id "NP_254255.1"; db_xref "GI:15600761"; db_xref "GeneID:878127"; product "inner membrane protein translocase subunit YidC";
NC_002516.2 genbank gene 6263805 6264212 . - 0 gene_id "rnpA"; transcript_id "rnpA"; gene_id "rnpA"; db_xref "GeneID:877910"; product "";
NC_002516.2 genbank CDS 6263805 6264212 . - 0 gene_id "rnpA"; transcript_id "rnpA"; gene_id "rnpA"; protein_id "NP_254256.1"; db_xref "GI:15600762"; db_xref "GeneID:877910"; product "ribonuclease P";
NC_002516.2 genbank gene 6264227 6264361 . - 0 gene_id "rpmH"; transcript_id "rpmH"; gene_id "rpmH"; db_xref "GeneID:877911"; product "";
NC_002516.2 genbank CDS 6264227 6264361 . - 0 gene_id "rpmH"; transcript_id "rpmH"; gene_id "rpmH"; protein_id "NP_254257.1"; db_xref "GI:15600763"; db_xref "GeneID:877911"; product "50S ribosomal protein L34";
bio-0.13.3/go.mod 0000664 0000000 0000000 00000001703 14573550650 0013470 0 ustar 00root root 0000000 0000000 module github.com/shenwei356/bio
go 1.17
require (
github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8
github.com/edsrzf/mmap-go v1.0.0
github.com/elliotwutingfeng/asciiset v0.0.0-20230602022725-51bbb787efab
github.com/shenwei356/breader v0.3.2
github.com/shenwei356/kmers v0.1.0
github.com/shenwei356/util v0.5.0
github.com/shenwei356/xopen v0.3.2
github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553
github.com/will-rowe/nthash v0.4.0
github.com/zeebo/wyhash v0.0.1
)
require (
github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 // indirect
github.com/dsnet/compress v0.0.1 // indirect
github.com/klauspost/compress v1.16.3 // indirect
github.com/klauspost/pgzip v1.2.5 // indirect
github.com/kr/pretty v0.3.1 // indirect
github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
github.com/ulikunitz/xz v0.5.11 // indirect
golang.org/x/sys v0.0.0-20220412211240-33da011f77ad // indirect
)
bio-0.13.3/go.sum 0000664 0000000 0000000 00000170523 14573550650 0013524 0 ustar 00root root 0000000 0000000 cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU=
cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU=
cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY=
cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc=
cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0=
cloud.google.com/go v0.50.0/go.mod h1:r9sluTvynVuxRIOHXQEHMFffphuXHOMZMycpNR5e6To=
cloud.google.com/go v0.52.0/go.mod h1:pXajvRH/6o3+F9jDHZWQ5PbGhn+o8w9qiu/CffaVdO4=
cloud.google.com/go v0.53.0/go.mod h1:fp/UouUEsRkN6ryDKNW/Upv/JBKnv6WDthjR6+vze6M=
cloud.google.com/go v0.54.0/go.mod h1:1rq2OEkV3YMf6n/9ZvGWI3GWw0VoqH/1x2nd8Is/bPc=
cloud.google.com/go v0.56.0/go.mod h1:jr7tqZxxKOVYizybht9+26Z/gUq7tiRzu+ACVAMbKVk=
cloud.google.com/go v0.57.0/go.mod h1:oXiQ6Rzq3RAkkY7N6t3TcE6jE+CIBBbA36lwQ1JyzZs=
cloud.google.com/go v0.62.0/go.mod h1:jmCYTdRCQuc1PHIIJ/maLInMho30T/Y0M4hTdTShOYc=
cloud.google.com/go v0.65.0/go.mod h1:O5N8zS7uWy9vkA9vayVHs65eM1ubvY4h553ofrNHObY=
cloud.google.com/go v0.72.0/go.mod h1:M+5Vjvlc2wnp6tjzE102Dw08nGShTscUx2nZMufOKPI=
cloud.google.com/go v0.74.0/go.mod h1:VV1xSbzvo+9QJOxLDaJfTjx5e+MePCpCWwvftOeQmWk=
cloud.google.com/go v0.78.0/go.mod h1:QjdrLG0uq+YwhjoVOLsS1t7TW8fs36kLs4XO5R5ECHg=
cloud.google.com/go v0.79.0/go.mod h1:3bzgcEeQlzbuEAYu4mrWhKqWjmpprinYgKJLgKHnbb8=
cloud.google.com/go v0.81.0/go.mod h1:mk/AM35KwGk/Nm2YSeZbxXdrNK3KZOYHmLkOqC2V6E0=
cloud.google.com/go/bigquery v1.0.1/go.mod h1:i/xbL2UlR5RvWAURpBYZTtm/cXjCha9lbfbpx4poX+o=
cloud.google.com/go/bigquery v1.3.0/go.mod h1:PjpwJnslEMmckchkHFfq+HTD2DmtT67aNFKH1/VBDHE=
cloud.google.com/go/bigquery v1.4.0/go.mod h1:S8dzgnTigyfTmLBfrtrhyYhwRxG72rYxvftPBK2Dvzc=
cloud.google.com/go/bigquery v1.5.0/go.mod h1:snEHRnqQbz117VIFhE8bmtwIDY80NLUZUMb4Nv6dBIg=
cloud.google.com/go/bigquery v1.7.0/go.mod h1://okPTzCYNXSlb24MZs83e2Do+h+VXtc4gLoIoXIAPc=
cloud.google.com/go/bigquery v1.8.0/go.mod h1:J5hqkt3O0uAFnINi6JXValWIb1v0goeZM77hZzJN/fQ=
cloud.google.com/go/datastore v1.0.0/go.mod h1:LXYbyblFSglQ5pkeyhO+Qmw7ukd3C+pD7TKLgZqpHYE=
cloud.google.com/go/datastore v1.1.0/go.mod h1:umbIZjpQpHh4hmRpGhH4tLFup+FVzqBi1b3c64qFpCk=
cloud.google.com/go/firestore v1.1.0/go.mod h1:ulACoGHTpvq5r8rxGJ4ddJZBZqakUQqClKRT5SZwBmk=
cloud.google.com/go/pubsub v1.0.1/go.mod h1:R0Gpsv3s54REJCy4fxDixWD93lHJMoZTyQ2kNxGRt3I=
cloud.google.com/go/pubsub v1.1.0/go.mod h1:EwwdRX2sKPjnvnqCa270oGRyludottCI76h+R3AArQw=
cloud.google.com/go/pubsub v1.2.0/go.mod h1:jhfEVHT8odbXTkndysNHCcx0awwzvfOlguIAii9o8iA=
cloud.google.com/go/pubsub v1.3.1/go.mod h1:i+ucay31+CNRpDW4Lu78I4xXG+O1r/MAHgjpRVR+TSU=
cloud.google.com/go/storage v1.0.0/go.mod h1:IhtSnM/ZTZV8YYJWCY8RULGVqBDmpoyjwiyrjsg+URw=
cloud.google.com/go/storage v1.5.0/go.mod h1:tpKbwo567HUNpVclU5sGELwQWBDZ8gh0ZeosJ0Rtdos=
cloud.google.com/go/storage v1.6.0/go.mod h1:N7U0C8pVQ/+NIKOBQyamJIeKQKkZ+mxpohlUTyfDhBk=
cloud.google.com/go/storage v1.8.0/go.mod h1:Wv1Oy7z6Yz3DshWRJFhqM/UCfaWIRTdp0RXyy7KQOVs=
cloud.google.com/go/storage v1.10.0/go.mod h1:FLPqc6j+Ki4BU591ie1oL6qBQGu2Bl/tZ9ullr3+Kg0=
dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU=
github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
github.com/antihax/optional v1.0.0/go.mod h1:uupD/76wgC+ih3iEmQUL+0Ugr19nfwCT1kdvxnR2qWY=
github.com/armon/circbuf v0.0.0-20150827004946-bbbad097214e/go.mod h1:3U/XgcO3hCbHZ8TKRvWD2dDTCfh9M9ya+I9JpbB7O8o=
github.com/armon/go-metrics v0.0.0-20180917152333-f0300d1749da/go.mod h1:Q73ZrmVTwzkszR9V5SSuryQ31EELlFMUz1kKyl939pY=
github.com/armon/go-radix v0.0.0-20180808171621-7fddfc383310/go.mod h1:ufUuZ+zHj4x4TnLV4JWEpy2hxWSpsRywHrMgIH9cCH8=
github.com/bgentry/speakeasy v0.1.0/go.mod h1:+zsyZBPWlz7T6j88CTgSN5bM796AkVf0kBD4zp0CCIs=
github.com/bketelsen/crypt v0.0.4/go.mod h1:aI6NrJ0pMGgvZKL1iVgXLnfIFJtfV+bKCoqOes/6LfM=
github.com/census-instrumentation/opencensus-proto v0.2.1/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU=
github.com/chzyer/logex v1.1.10/go.mod h1:+Ywpsq7O8HXn0nuIou7OrIPyXbp3wmkHB+jjWRnGsAI=
github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e/go.mod h1:nSuG5e5PlCu98SY8svDHJxuZscDgtXS6KTTbou5AhLI=
github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU=
github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw=
github.com/cncf/udpa/go v0.0.0-20191209042840-269d4d468f6f/go.mod h1:M8M6+tZqaGXZJjfX53e64911xZQV5JYwmTeXPW+k8Sc=
github.com/cncf/udpa/go v0.0.0-20200629203442-efcf912fb354/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk=
github.com/cncf/udpa/go v0.0.0-20201120205902-5459f2c99403/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk=
github.com/coreos/go-semver v0.3.0/go.mod h1:nnelYz7RCh+5ahJtPPxZlU+153eP4D4r3EedlOD2RNk=
github.com/coreos/go-systemd/v22 v22.3.2/go.mod h1:Y58oyj3AT4RCenI/lSvhwexgC+NSVTIJ3seZv2GcEnc=
github.com/cpuguy83/go-md2man/v2 v2.0.0/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU=
github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 h1:iwZdTE0PVqJCos1vaoKsclOGD3ADKpshg3SRtYBbwso=
github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548/go.mod h1:e6NPNENfs9mPDVNRekM7lKScauxd5kXTr1Mfyig6TDM=
github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8 h1:LpMLYGyy67BoAFGda1NeOBQwqlv7nUXpm+rIVHGxZZ4=
github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8/go.mod h1:q2w6Bg5jeox1B+QkJ6Wp/+Vn0G/bo3f1uY7Fn3vivIQ=
github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
github.com/dsnet/compress v0.0.1 h1:PlZu0n3Tuv04TzpfPbrnI0HW/YwodEXDS+oPKahKF0Q=
github.com/dsnet/compress v0.0.1/go.mod h1:Aw8dCMJ7RioblQeTqt88akK31OvO8Dhf5JflhBbQEHo=
github.com/dsnet/golib v0.0.0-20171103203638-1ea166775780/go.mod h1:Lj+Z9rebOhdfkVLjJ8T6VcRQv3SXugXy999NBtR9aFY=
github.com/edsrzf/mmap-go v1.0.0 h1:CEBF7HpRnUCSJgGUb5h1Gm7e3VkmVDrR8lvWVLtrOFw=
github.com/edsrzf/mmap-go v1.0.0/go.mod h1:YO35OhQPt3KJa3ryjFM5Bs14WD66h8eGKpfaBNrHW5M=
github.com/elliotwutingfeng/asciiset v0.0.0-20230602022725-51bbb787efab h1:h1UgjJdAAhj+uPL68n7XASS6bU+07ZX1WJvVS2eyoeY=
github.com/elliotwutingfeng/asciiset v0.0.0-20230602022725-51bbb787efab/go.mod h1:GLo/8fDswSAniFG+BFIaiSPcK610jyzgEhWYPQwuQdw=
github.com/envoyproxy/go-control-plane v0.9.0/go.mod h1:YTl/9mNaCwkRvm6d1a2C3ymFceY/DCBVvsKhRF0iEA4=
github.com/envoyproxy/go-control-plane v0.9.1-0.20191026205805-5f8ba28d4473/go.mod h1:YTl/9mNaCwkRvm6d1a2C3ymFceY/DCBVvsKhRF0iEA4=
github.com/envoyproxy/go-control-plane v0.9.4/go.mod h1:6rpuAdCZL397s3pYoYcLgu1mIlRU8Am5FuJP05cCM98=
github.com/envoyproxy/go-control-plane v0.9.7/go.mod h1:cwu0lG7PUMfa9snN8LXBig5ynNVH9qI8YYLbd1fK2po=
github.com/envoyproxy/go-control-plane v0.9.9-0.20201210154907-fd9021fe5dad/go.mod h1:cXg6YxExXjJnVBQHBLXeUAgxn2UodCpnH306RInaBQk=
github.com/envoyproxy/go-control-plane v0.9.9-0.20210217033140-668b12f5399d/go.mod h1:cXg6YxExXjJnVBQHBLXeUAgxn2UodCpnH306RInaBQk=
github.com/envoyproxy/protoc-gen-validate v0.1.0/go.mod h1:iSmxcyjqTsJpI2R4NaDN7+kN2VEUnK/pcBlmesArF7c=
github.com/fatih/color v1.7.0/go.mod h1:Zm6kSWBoL9eyXnKyktHP6abPY2pDugNf5KwzbycvMj4=
github.com/fsnotify/fsnotify v1.4.9/go.mod h1:znqG4EE+3YCdAaPaxE2ZRY/06pZUdp0tY4IgpuI1SZQ=
github.com/ghodss/yaml v1.0.0/go.mod h1:4dBDuWmgqj2HViK6kFavaiC9ZROes6MMH2rRYeMEF04=
github.com/go-gl/glfw v0.0.0-20190409004039-e6da0acd62b1/go.mod h1:vR7hzQXu2zJy9AVAgeJqvqgH9Q5CA+iKCZ2gyEVpxRU=
github.com/go-gl/glfw/v3.3/glfw v0.0.0-20191125211704-12ad95a8df72/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8=
github.com/go-gl/glfw/v3.3/glfw v0.0.0-20200222043503-6f7a984d4dc4/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8=
github.com/godbus/dbus/v5 v5.0.4/go.mod h1:xhWf0FNVPg57R7Z0UbKHbJfkEywrmjJnf7w5xrFpKfA=
github.com/gogo/protobuf v1.3.2/go.mod h1:P1XiOD3dCwIKUDQYPy72D8LYyHL2YPYrpS2s69NZV8Q=
github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q=
github.com/golang/groupcache v0.0.0-20190702054246-869f871628b6/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc=
github.com/golang/groupcache v0.0.0-20191227052852-215e87163ea7/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc=
github.com/golang/groupcache v0.0.0-20200121045136-8c9f03a8e57e/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc=
github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A=
github.com/golang/mock v1.2.0/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A=
github.com/golang/mock v1.3.1/go.mod h1:sBzyDLLjw3U8JLTeZvSv8jJB+tU5PVekmnlKIyFUx0Y=
github.com/golang/mock v1.4.0/go.mod h1:UOMv5ysSaYNkG+OFQykRIcU/QvvxJf3p21QfJ2Bt3cw=
github.com/golang/mock v1.4.1/go.mod h1:UOMv5ysSaYNkG+OFQykRIcU/QvvxJf3p21QfJ2Bt3cw=
github.com/golang/mock v1.4.3/go.mod h1:UOMv5ysSaYNkG+OFQykRIcU/QvvxJf3p21QfJ2Bt3cw=
github.com/golang/mock v1.4.4/go.mod h1:l3mdAwkq5BuhzHwde/uurv3sEJeZMXNpwsxVWU71h+4=
github.com/golang/mock v1.5.0/go.mod h1:CWnOUgYIOo4TcNZ0wHX3YZCqsaM1I1Jvs6v3mP3KVu8=
github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
github.com/golang/protobuf v1.3.2/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
github.com/golang/protobuf v1.3.3/go.mod h1:vzj43D7+SQXF/4pzW/hwtAqwc6iTitCiVSaWz5lYuqw=
github.com/golang/protobuf v1.3.4/go.mod h1:vzj43D7+SQXF/4pzW/hwtAqwc6iTitCiVSaWz5lYuqw=
github.com/golang/protobuf v1.3.5/go.mod h1:6O5/vntMXwX2lRkT1hjjk0nAC1IDOTvTlVgjlRvqsdk=
github.com/golang/protobuf v1.4.0-rc.1/go.mod h1:ceaxUfeHdC40wWswd/P6IGgMaK3YpKi5j83Wpe3EHw8=
github.com/golang/protobuf v1.4.0-rc.1.0.20200221234624-67d41d38c208/go.mod h1:xKAWHe0F5eneWXFV3EuXVDTCmh+JuBKY0li0aMyXATA=
github.com/golang/protobuf v1.4.0-rc.2/go.mod h1:LlEzMj4AhA7rCAGe4KMBDvJI+AwstrUpVNzEA03Pprs=
github.com/golang/protobuf v1.4.0-rc.4.0.20200313231945-b860323f09d0/go.mod h1:WU3c8KckQ9AFe+yFwt9sWVRKCVIyN9cPHBJSNnbL67w=
github.com/golang/protobuf v1.4.0/go.mod h1:jodUvKwWbYaEsadDk5Fwe5c77LiNKVO9IDvqG2KuDX0=
github.com/golang/protobuf v1.4.1/go.mod h1:U8fpvMrcmy5pZrNK1lt4xCsGvpyWQ/VVv6QDs8UjoX8=
github.com/golang/protobuf v1.4.2/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw735rRwI=
github.com/golang/protobuf v1.4.3/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw735rRwI=
github.com/golang/protobuf v1.5.0/go.mod h1:FsONVRAS9T7sI+LIUmWTfcYkHO4aIWwzhcaSAoJOfIk=
github.com/golang/protobuf v1.5.1/go.mod h1:DopwsBzvsk0Fs44TXzsVbJyPhcCPeIwnvohx4u74HPM=
github.com/golang/protobuf v1.5.2/go.mod h1:XVQd3VNwM+JqD3oG2Ue2ip4fOMUkwXdXDdiuN0vRsmY=
github.com/google/btree v0.0.0-20180813153112-4030bb1f1f0c/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=
github.com/google/btree v1.0.0/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=
github.com/google/go-cmp v0.2.0/go.mod h1:oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M=
github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU=
github.com/google/go-cmp v0.3.1/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU=
github.com/google/go-cmp v0.4.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
github.com/google/go-cmp v0.4.1/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
github.com/google/go-cmp v0.5.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
github.com/google/go-cmp v0.5.1/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
github.com/google/go-cmp v0.5.2/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
github.com/google/go-cmp v0.5.3/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
github.com/google/go-cmp v0.5.4/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
github.com/google/go-cmp v0.5.5/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
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github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553 h1:DRC1ubdb3ZmyyIeCSTxjZIQAnpLPfKVgYrLETQuOPjo=
github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553/go.mod h1:Rj7Csq/tZ/egz+Ltc2IVpsA5309AmSMEswjkTZmq2Xc=
github.com/ulikunitz/xz v0.5.6/go.mod h1:2bypXElzHzzJZwzH67Y6wb67pO62Rzfn7BSiF4ABRW8=
github.com/ulikunitz/xz v0.5.10/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14=
github.com/ulikunitz/xz v0.5.11 h1:kpFauv27b6ynzBNT/Xy+1k+fK4WswhN/6PN5WhFAGw8=
github.com/ulikunitz/xz v0.5.11/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14=
github.com/will-rowe/nthash v0.4.0 h1:YiHdqR0phP9o/kKVMJJiuXYY9qOH8QHofptDqUCOxrU=
github.com/will-rowe/nthash v0.4.0/go.mod h1:5ezweuK0J5j+/7lih/RkrSmnxI3hoaPpQiVWJ7rd960=
github.com/yuin/goldmark v1.1.25/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
github.com/yuin/goldmark v1.1.27/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
github.com/yuin/goldmark v1.1.32/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
github.com/yuin/goldmark v1.2.1/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
github.com/yuin/goldmark v1.3.5/go.mod h1:mwnBkeHKe2W/ZEtQ+71ViKU8L12m81fl3OWwC1Zlc8k=
github.com/zeebo/wyhash v0.0.1 h1:VEByEMek3iHhV65CgG3SRAWVtg/6TcmbEKj5jPOKDrc=
github.com/zeebo/wyhash v0.0.1/go.mod h1:Ti+OwfNtM5AZiYAL0kOPIfliqDP5c0VtOnnMAqzuuZk=
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go.etcd.io/etcd/client/pkg/v3 v3.5.0/go.mod h1:IJHfcCEKxYu1Os13ZdwCwIUTUVGYTSAM3YSwc9/Ac1g=
go.etcd.io/etcd/client/v2 v2.305.0/go.mod h1:h9puh54ZTgAKtEbut2oe9P4L/oqKCVB6xsXlzd7alYQ=
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go.opencensus.io v0.22.0/go.mod h1:+kGneAE2xo2IficOXnaByMWTGM9T73dGwxeWcUqIpI8=
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golang.org/x/crypto v0.0.0-20181029021203-45a5f77698d3/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4=
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golang.org/x/crypto v0.0.0-20190510104115-cbcb75029529/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
golang.org/x/crypto v0.0.0-20190605123033-f99c8df09eb5/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
golang.org/x/crypto v0.0.0-20190820162420-60c769a6c586/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
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golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9/go.mod h1:LzIPMQfyMNhhGPhUkYOs5KpL4U8rLKemX1yGLhDgUto=
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golang.org/x/exp v0.0.0-20190829153037-c13cbed26979/go.mod h1:86+5VVa7VpoJ4kLfm080zCjGlMRFzhUhsZKEZO7MGek=
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golang.org/x/exp v0.0.0-20200207192155-f17229e696bd/go.mod h1:J/WKrq2StrnmMY6+EHIKF9dgMWnmCNThgcyBT1FY9mM=
golang.org/x/exp v0.0.0-20200224162631-6cc2880d07d6/go.mod h1:3jZMyOhIsHpP37uCMkUooju7aAi5cS1Q23tOzKc+0MU=
golang.org/x/image v0.0.0-20190227222117-0694c2d4d067/go.mod h1:kZ7UVZpmo3dzQBMxlp+ypCbDeSB+sBbTgSJuh5dn5js=
golang.org/x/image v0.0.0-20190802002840-cff245a6509b/go.mod h1:FeLwcggjj3mMvU+oOTbSwawSJRM1uh48EjtB4UJZlP0=
golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE=
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golang.org/x/lint v0.0.0-20191125180803-fdd1cda4f05f/go.mod h1:5qLYkcX4OjUUV8bRuDixDT3tpyyb+LUpUlRWLxfhWrs=
golang.org/x/lint v0.0.0-20200130185559-910be7a94367/go.mod h1:3xt1FjdF8hUf6vQPIChWIBhFzV8gjjsPE/fR3IyQdNY=
golang.org/x/lint v0.0.0-20200302205851-738671d3881b/go.mod h1:3xt1FjdF8hUf6vQPIChWIBhFzV8gjjsPE/fR3IyQdNY=
golang.org/x/lint v0.0.0-20201208152925-83fdc39ff7b5/go.mod h1:3xt1FjdF8hUf6vQPIChWIBhFzV8gjjsPE/fR3IyQdNY=
golang.org/x/lint v0.0.0-20210508222113-6edffad5e616/go.mod h1:3xt1FjdF8hUf6vQPIChWIBhFzV8gjjsPE/fR3IyQdNY=
golang.org/x/mobile v0.0.0-20190312151609-d3739f865fa6/go.mod h1:z+o9i4GpDbdi3rU15maQ/Ox0txvL9dWGYEHz965HBQE=
golang.org/x/mobile v0.0.0-20190719004257-d2bd2a29d028/go.mod h1:E/iHnbuqvinMTCcRqshq8CkpyQDoeVncDDYHnLhea+o=
golang.org/x/mod v0.0.0-20190513183733-4bf6d317e70e/go.mod h1:mXi4GBBbnImb6dmsKGUJ2LatrhH/nqhxcFungHvyanc=
golang.org/x/mod v0.1.0/go.mod h1:0QHyrYULN0/3qlju5TqG8bIK38QM8yzMo5ekMj3DlcY=
golang.org/x/mod v0.1.1-0.20191105210325-c90efee705ee/go.mod h1:QqPTAvyqsEbceGzBzNggFXnrqF1CaUcvgkdR5Ot7KZg=
golang.org/x/mod v0.1.1-0.20191107180719-034126e5016b/go.mod h1:QqPTAvyqsEbceGzBzNggFXnrqF1CaUcvgkdR5Ot7KZg=
golang.org/x/mod v0.2.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
golang.org/x/mod v0.3.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
golang.org/x/mod v0.4.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
golang.org/x/mod v0.4.1/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
golang.org/x/mod v0.4.2/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
golang.org/x/net v0.0.0-20180724234803-3673e40ba225/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
golang.org/x/net v0.0.0-20180826012351-8a410e7b638d/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
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golang.org/x/net v0.0.0-20181201002055-351d144fa1fc/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
golang.org/x/net v0.0.0-20190108225652-1e06a53dbb7e/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
golang.org/x/net v0.0.0-20190213061140-3a22650c66bd/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
golang.org/x/net v0.0.0-20190501004415-9ce7a6920f09/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
golang.org/x/net v0.0.0-20190503192946-f4e77d36d62c/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
golang.org/x/net v0.0.0-20190603091049-60506f45cf65/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks=
golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20190628185345-da137c7871d7/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20190724013045-ca1201d0de80/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20191209160850-c0dbc17a3553/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20200114155413-6afb5195e5aa/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20200202094626-16171245cfb2/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20200222125558-5a598a2470a0/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20200226121028-0de0cce0169b/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20200301022130-244492dfa37a/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20200324143707-d3edc9973b7e/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A=
golang.org/x/net v0.0.0-20200501053045-e0ff5e5a1de5/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A=
golang.org/x/net v0.0.0-20200506145744-7e3656a0809f/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A=
golang.org/x/net v0.0.0-20200513185701-a91f0712d120/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A=
golang.org/x/net v0.0.0-20200520182314-0ba52f642ac2/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A=
golang.org/x/net v0.0.0-20200625001655-4c5254603344/go.mod h1:/O7V0waA8r7cgGh81Ro3o1hOxt32SMVPicZroKQ2sZA=
golang.org/x/net v0.0.0-20200707034311-ab3426394381/go.mod h1:/O7V0waA8r7cgGh81Ro3o1hOxt32SMVPicZroKQ2sZA=
golang.org/x/net v0.0.0-20200822124328-c89045814202/go.mod h1:/O7V0waA8r7cgGh81Ro3o1hOxt32SMVPicZroKQ2sZA=
golang.org/x/net v0.0.0-20201021035429-f5854403a974/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU=
golang.org/x/net v0.0.0-20201031054903-ff519b6c9102/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU=
golang.org/x/net v0.0.0-20201110031124-69a78807bb2b/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU=
golang.org/x/net v0.0.0-20201209123823-ac852fbbde11/go.mod h1:m0MpNAwzfU5UDzcl9v0D8zg8gWTRqZa9RBIspLL5mdg=
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golang.org/x/oauth2 v0.0.0-20190226205417-e64efc72b421/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw=
golang.org/x/oauth2 v0.0.0-20190604053449-0f29369cfe45/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw=
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golang.org/x/oauth2 v0.0.0-20200902213428-5d25da1a8d43/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A=
golang.org/x/oauth2 v0.0.0-20201109201403-9fd604954f58/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A=
golang.org/x/oauth2 v0.0.0-20201208152858-08078c50e5b5/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A=
golang.org/x/oauth2 v0.0.0-20210218202405-ba52d332ba99/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A=
golang.org/x/oauth2 v0.0.0-20210220000619-9bb904979d93/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A=
golang.org/x/oauth2 v0.0.0-20210313182246-cd4f82c27b84/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A=
golang.org/x/oauth2 v0.0.0-20210402161424-2e8d93401602/go.mod h1:KelEdhl1UZF7XfJ4dDtk6s++YSgaE7mD/BuKKDLBl4A=
golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
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rsc.io/quote/v3 v3.1.0/go.mod h1:yEA65RcK8LyAZtP9Kv3t0HmxON59tX3rD+tICJqUlj0=
rsc.io/sampler v1.3.0/go.mod h1:T1hPZKmBbMNahiBKFy5HrXp6adAjACjK9JXDnKaTXpA=
bio-0.13.3/seq/ 0000775 0000000 0000000 00000000000 14573550650 0013151 5 ustar 00root root 0000000 0000000 bio-0.13.3/seq/README.md 0000775 0000000 0000000 00000000705 14573550650 0014435 0 ustar 00root root 0000000 0000000 # seq
[](https://pkg.go.dev/github.com/shenwei356/bio/seq)
This package defines `Seq` and `Alphabet` type, and provides some basic operations of sequence,
like validation of DNA/RNA/Protein sequence, getting reverse complement sequence and translation of RNA to protein.
This package was inspired by
[biogo](https://github.com/biogo/biogo/blob/master/alphabet/alphabet.go).
bio-0.13.3/seq/alphabet.go 0000775 0000000 0000000 00000023103 14573550650 0015262 0 ustar 00root root 0000000 0000000 /*
Package seq defines a *Seq* type, and provides some basic operations of sequence,
like validation of DNA/RNA/Protein sequence and getting reverse complement sequence.
This package was inspired by
[biogo](https://code.google.com/p/biogo/source/browse/#git%2Falphabet).
IUPAC nucleotide code: ACGTURYSWKMBDHVN
http://droog.gs.washington.edu/parc/images/iupac.html
code base Complement
A A T
C C G
G G C
T/U T A
M A/C K
R A/G Y
W A/T W
S C/G S
Y C/T R
K G/T M
V A/C/G B
H A/C/T D
D A/G/T H
B C/G/T V
X/N A/C/G/T X
. not A/C/G/T
or- gap
IUPAC amino acid code
A Ala Alanine
B Asx Aspartic acid or Asparagine [2]
C Cys Cysteine
D Asp Aspartic Acid
E Glu Glutamic Acid
F Phe Phenylalanine
G Gly Glycine
H His Histidine
I Ile Isoleucine
J Isoleucine or Leucine [4]
K Lys Lysine
L Leu Leucine
M Met Methionine
N Asn Asparagine
O pyrrolysine [6]
P Pro Proline
Q Gln Glutamine
R Arg Arginine
S Ser Serine
T Thr Threonine
U Sec selenocysteine [5,6]
V Val Valine
W Trp Tryptophan
Y Tyr Tyrosine
Z Glx Glutamine or Glutamic acid [2]
X unknown amino acid
. gaps
* End
Reference:
1. http://www.bioinformatics.org/sms/iupac.html
2. http://www.dnabaser.com/articles/IUPAC%20ambiguity%20codes.html
3. http://www.bioinformatics.org/sms2/iupac.html
4. http://www.matrixscience.com/blog/non-standard-amino-acid-residues.html
5. http://www.sbcs.qmul.ac.uk/iupac/AminoAcid/A2021.html#AA21
6. https://en.wikipedia.org/wiki/Amino_acid
*/
package seq
import (
"errors"
"fmt"
"runtime"
"sync"
"github.com/elliotwutingfeng/asciiset"
"github.com/shenwei356/util/byteutil"
)
/*
Alphabet could be defined. Attention that,
**the letters are case sensitive**.
For example, DNA:
DNA, _ = NewAlphabet(
"DNA",
[]byte("acgtACGT"),
[]byte("tgcaTGCA"),
[]byte(" -"),
[]byte("nN"))
*/
type Alphabet struct {
t string
isUnlimit bool
letters []byte
pairs []byte
gap []byte
ambiguous []byte
allLetters []byte
pairLetters []byte
}
// NewAlphabet is Constructor for type *Alphabet*
func NewAlphabet(
t string,
isUnlimit bool,
letters []byte,
pairs []byte,
gap []byte,
ambiguous []byte,
) (*Alphabet, error) {
a := &Alphabet{t, isUnlimit, letters, pairs, gap, ambiguous, []byte{}, []byte{}}
if isUnlimit {
return a, nil
}
if len(letters) != len(pairs) {
return a, errors.New("mismatch of length of letters and pairs")
}
for i := 0; i < len(letters); i++ {
a.allLetters = append(a.allLetters, letters[i])
}
// add gap and ambiguous code
a.allLetters = append(a.allLetters, gap...)
a.allLetters = append(a.allLetters, ambiguous...)
// construct special slice.
// index are the integer of a byte, and value is the original byte.
// it's faster than map!!!!
max := -1
for i := 0; i < len(a.allLetters); i++ {
b := int(a.allLetters[i])
if max < b {
max = b
}
}
a.pairLetters = make([]byte, max+1)
for i := 0; i < len(letters); i++ {
a.pairLetters[letters[i]-'\x00'] = pairs[i]
}
for _, v := range gap {
a.pairLetters[v-'\x00'] = v
}
for _, v := range ambiguous {
a.pairLetters[v-'\x00'] = v
}
return a, nil
}
// Clone of a Alphabet
func (a *Alphabet) Clone() *Alphabet {
return &Alphabet{
t: a.t,
isUnlimit: a.isUnlimit,
letters: []byte(string(a.letters)),
pairs: []byte(string(a.pairs)),
gap: []byte(string(a.gap)),
ambiguous: []byte(string(a.ambiguous)),
allLetters: []byte(string(a.allLetters)),
pairLetters: []byte(string(a.pairLetters)),
}
}
// Type returns type of the alphabet
func (a *Alphabet) Type() string {
return a.t
}
// Letters returns letters
func (a *Alphabet) Letters() []byte {
return a.letters
}
// Gaps returns gaps
func (a *Alphabet) Gaps() []byte {
return a.gap
}
// AmbiguousLetters returns AmbiguousLetters
func (a *Alphabet) AmbiguousLetters() []byte {
return a.ambiguous
}
// AllLetters return all letters
func (a *Alphabet) AllLetters() []byte {
return a.allLetters
}
// String returns type of the alphabet
func (a *Alphabet) String() string {
return a.t
}
// IsValidLetter is used to validate a letter
func (a *Alphabet) IsValidLetter(b byte) bool {
if a.isUnlimit {
return true
}
i := int(b)
if i >= len(a.pairLetters) {
return false
}
return a.pairLetters[i] != 0
}
// ValidSeqLengthThreshold is the threshold of sequence length that
// needed to parallelly checking sequence
var ValidSeqLengthThreshold = 10000
// ValidSeqThreads is the threads number of parallelly checking sequence
var ValidSeqThreads = runtime.NumCPU()
type seqCheckStatus struct {
err error
}
// IsValid is used to validate a byte slice
func (a *Alphabet) IsValid(s []byte) error {
if len(s) == 0 {
return nil
}
if a == nil || a.isUnlimit {
return nil
}
l := len(s)
var i int
if l < ValidSeqLengthThreshold {
for _, b := range s {
i = int(b)
if i >= len(a.pairLetters) || a.pairLetters[i] == 0 {
return fmt.Errorf("seq: invalid %s letter: %s", a, []byte{b})
}
}
return nil
}
chunkSize, start, end := int(l/ValidSeqThreads)+1, 0, 0
var wg sync.WaitGroup
tokens := make(chan int, ValidSeqThreads)
ch := make(chan seqCheckStatus, ValidSeqThreads)
done := make(chan struct{})
var once sync.Once
finished := false
for i := 0; i < ValidSeqThreads; i++ {
start = i * chunkSize
end = (i + 1) * chunkSize
if end > l {
end = l
}
tokens <- 1
wg.Add(1)
go func(start, end int) {
defer func() {
<-tokens
wg.Done()
}()
select {
case <-done:
if !finished {
finished = true
// close(ch)
return
}
default:
}
var j int
for i := start; i < end; i++ {
j = int(s[i])
if j >= len(a.pairLetters) || a.pairLetters[j] == 0 {
ch <- seqCheckStatus{fmt.Errorf("seq: invalid %s lebtter: %s at %d", a, []byte{s[i]}, i)}
once.Do(func() {
close(done)
})
return
}
}
ch <- seqCheckStatus{nil}
}(start, end)
}
wg.Wait()
close(ch)
for status := range ch {
if status.err != nil {
return status.err
}
}
return nil
}
// PairLetter return the Pair Letter
func (a *Alphabet) PairLetter(b byte) (byte, error) {
if a.isUnlimit {
return b, nil
}
if int(b) >= len(a.pairLetters) {
return b, fmt.Errorf("seq: invalid letter: %c", b)
}
p := a.pairLetters[b-'\x00']
if p == 0 {
return b, fmt.Errorf("seq: invalid letter: %c", b)
}
return p, nil
}
/*
Four types of alphabets are pre-defined:
DNA Deoxyribonucleotide code
DNAredundant DNA + Ambiguity Codes
RNA Oxyribonucleotide code
RNAredundant RNA + Ambiguity Codes
Protein Amino Acide single-letter Code
Unlimit Self-defined, including all 26 English letters
*/
var (
DNA *Alphabet
DNAredundant *Alphabet
RNA *Alphabet
RNAredundant *Alphabet
Protein *Alphabet
Unlimit *Alphabet
abProtein asciiset.ASCIISet
abDNAredundant asciiset.ASCIISet
abDNA asciiset.ASCIISet
abRNAredundant asciiset.ASCIISet
abRNA asciiset.ASCIISet
)
func init() {
DNA, _ = NewAlphabet(
"DNA",
false,
[]byte("acgtACGT"),
[]byte("tgcaTGCA"),
[]byte(" -."),
[]byte("nN."))
DNAredundant, _ = NewAlphabet(
"DNAredundant",
false,
[]byte("acgtryswkmbdhvACGTRYSWKMBDHV"),
[]byte("tgcayrswmkvhdbTGCAYRSWMKVHDB"),
[]byte(" -."),
[]byte("nN."))
RNA, _ = NewAlphabet(
"RNA",
false,
[]byte("acguACGU"),
[]byte("ugcaUGCA"),
[]byte(" -."),
[]byte("nN"))
RNAredundant, _ = NewAlphabet(
"RNAredundant",
false,
[]byte("acguryswkmbdhvACGURYSWKMBDHV"),
[]byte("ugcayrswmkvhdbUGCAYRSWMKVHDB"),
[]byte(" -."),
[]byte("nN"))
Protein, _ = NewAlphabet(
"Protein",
false,
[]byte("abcdefghijklmnopqrstuvwyzABCDEFGHIJKLMNOPQRSTUVWYZ"),
[]byte("abcdefghijklmnopqrstuvwyzABCDEFGHIJKLMNOPQRSTUVWYZ"),
[]byte(" -"),
[]byte("xX*_."))
Unlimit, _ = NewAlphabet(
"Unlimit",
true,
nil,
nil,
nil,
nil)
abProtein = slice2map(byteutil.Alphabet(Protein.AllLetters()))
abDNAredundant = slice2map(byteutil.Alphabet(DNAredundant.AllLetters()))
abDNA = slice2map(byteutil.Alphabet(DNA.AllLetters()))
abRNAredundant = slice2map(byteutil.Alphabet(RNAredundant.AllLetters()))
abRNA = slice2map(byteutil.Alphabet(RNA.AllLetters()))
}
// AlphabetGuessSeqLengthThreshold is the length of sequence prefix of the first FASTA record
// based which FastaRecord guesses the sequence type. 0 for whole seq
var AlphabetGuessSeqLengthThreshold = 10000
// GuessAlphabet guesses alphabet by given
func GuessAlphabet(seqs []byte) *Alphabet {
if len(seqs) == 0 {
return Unlimit
}
var alphabetMap asciiset.ASCIISet
if AlphabetGuessSeqLengthThreshold == 0 || len(seqs) <= AlphabetGuessSeqLengthThreshold {
alphabetMap = slice2map(byteutil.Alphabet(seqs))
} else { // reduce guessing time
alphabetMap = slice2map(byteutil.Alphabet(seqs[0:AlphabetGuessSeqLengthThreshold]))
}
if isSubset(alphabetMap, abDNA) {
return DNA
}
if isSubset(alphabetMap, abRNA) {
return RNA
}
if isSubset(alphabetMap, abDNAredundant) {
return DNAredundant
}
if isSubset(alphabetMap, abRNAredundant) {
return RNAredundant
}
if isSubset(alphabetMap, abProtein) {
return Protein
}
return Unlimit
}
// GuessAlphabetLessConservatively change DNA to DNAredundant and RNA to RNAredundant
func GuessAlphabetLessConservatively(seqs []byte) *Alphabet {
ab := GuessAlphabet(seqs)
if ab == DNA {
return DNAredundant
}
if ab == RNA {
return RNAredundant
}
return ab
}
// isSubset returns true if query is a subset of subject
func isSubset(query, subject asciiset.ASCIISet) bool {
// A ⊆ B iff (A ∪ B) = B
union := query.Union(subject)
return union.Equals(subject)
}
func slice2map(s []byte) asciiset.ASCIISet {
m, _ := asciiset.MakeASCIISet(string(s))
return m
}
bio-0.13.3/seq/alphabet_test.go 0000775 0000000 0000000 00000005116 14573550650 0016325 0 ustar 00root root 0000000 0000000 package seq
import (
"regexp"
"strings"
"testing"
)
func TestAlphabet(t *testing.T) {
dna := []byte("acgtACGT")
dna2 := []byte("ACGTRYSWKMBDHV")
rna := []byte("AUGCUUCCGGCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAU" +
"UGAUGCUUCACACCUGGGCUCUCCGGGUACCAGGACGGUUUGAGCAGAU")
rna2 := []byte("ACGURYSWKMBDHV")
protein := []byte(regexp.MustCompile(`\r?\n|\s`).ReplaceAllString(
`MGLNRFMRAMMVVFITANCITINPDIIFAATDSEDSSLNTDEWEEEKTEEQPSEVNTGPR
YETAREVSSRDIKELEKSNKVRNTNKADLIAMLKEKAEKGPNINNNNSEQTENAAINEEA
SGADRPAIQVERRHPGLPSDSAAEIKKRRKAIASSDSELESLTYPDKPTKVNKKKVAKES
VADASESDLDSSMQSADESSPQPLKANQQPFFPKVFKKIKDAGKWVRDKIDENPEVKKAI
VDKSAGLIDQLLTKKKSEEVNASDFPPPPTDEELRLALPETPMLLGFNAPATSEPSSFEF
PPPPTDEELRLALPETPMLLGFNAPATSEPSSFEFPPPPTEDELEIIRETASSLDSSFTR
GDLASLRNAINRHSQNFSDFPPIPTEEELNGRGGRPTSEEFSSLNSGDFTDDENSETTEE
EIDRLADLRDRGTGKHSRNAGFLPLNPFASSPVPSLSPKVSKISAPALISDITKKTPFKN
PSQPLNVFNKKTTTKTVTKKPTPVKTAPKLAELPATKPQETVLRENKTPFIEKQAETNKQ
SINMPSLPVIQKEATESDKEEMKPQTEEKMVEESESANNANGKNRSAGIEEGKLIAKSAE
DEKAKEEPGNHTTLILAMLAIGVFSLGAFIKIIQLRKNN`, ""))
ok := DNA.IsValid(dna) == nil &&
DNAredundant.IsValid(dna2) == nil &&
RNA.IsValid(rna) == nil &&
RNAredundant.IsValid(rna2) == nil &&
Protein.IsValid(protein) == nil
if !ok {
t.Error("validating sequence failed.")
return
}
// fmt.Println("protein", GuessAlphabet(protein))
// fmt.Println("dna2", GuessAlphabet(dna2))
// fmt.Println("dna", GuessAlphabet(dna))
// fmt.Println("rna2", GuessAlphabet(rna2))
// fmt.Println("rna", GuessAlphabet(rna))
ok = GuessAlphabet(dna) == DNA && GuessAlphabet(dna2) == DNAredundant && GuessAlphabet(rna) == RNA && GuessAlphabet(rna2) == RNAredundant && GuessAlphabet(protein) == Protein
if !ok {
t.Error("guessing alphabet error")
return
}
}
func TestAlphabet2(t *testing.T) {
s := regexp.MustCompile(`\r?\n|\s`).ReplaceAllString(
`MGLNRFMRAMMVVFITANCITINPDIIFAATDSEDSSLNTDEWEEEKTEEQPSEVNTGPR
YETAREVSSRDIKELEKSNKVRNTNKADLIAMLKEKAEKGPNINNNNSEQTENAAINEEA
SGADRPAIQVERRHPGLPSDSAAEIKKRRKAIASSDSELESLTYPDKPTKVNKKKVAKES
VADASESDLDSSMQSADESSPQPLKANQQPFFPKVFKKIKDAGKWVRDKIDENPEVKKAI
VDKSAGLIDQLLTKKKSEEVNASDFPPPPTDEELRLALPETPMLLGFNAPATSEPSSFEF
PPPPTDEELRLALPETPMLLGFNAPATSEPSSFEFPPPPTEDELEIIRETASSLDSSFTR
GDLASLRNAINRHSQNFSDFPPIPTEEELNGRGGRPTSEEFSSLNSGDFTDDENSETTEE
EIDRLADLRDRGTGKHSRNAGFLPLNPFASSPVPSLSPKVSKISAPALISDITKKTPFKN
PSQPLNVFNKKTTTKTVTKKPTPVKTAPKLAELPATKPQETVLRENKTPFIEKQAETNKQ
SINMPSLPVIQKEATESDKEEMKPQTEEKMVEESESANNANGKNRSAGIEEGKLIAKSAE
DEKAKEEPGNHTTLILAMLAIGVFSLGAFIKIIQLRKNN>`, "")
protein := []byte(strings.Repeat(s, 1000))
ok := Protein.IsValid(protein) == nil
if ok {
t.Error("validating sequence failed.")
return
}
}
bio-0.13.3/seq/ambiguous_bases.go 0000775 0000000 0000000 00000006770 14573550650 0016665 0 ustar 00root root 0000000 0000000 package seq
import "errors"
/*
base bases code
A A 1
C C 2
G G 4
T/U T 8
M A/C 3
R A/G 5
W A/T 9
S C/G 6
Y C/T 10
K G/T 12
V A/C/G 7
H A/C/T 11
D A/G/T 13
B C/G/T 14
N A/C/G/T 15
*/
var code2base = [16]byte{'-', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'}
// ErrInvalidDNABase means invalid DNA base
var ErrInvalidDNABase = errors.New("seq: invalid DNA base")
func base2code(b byte) (int, error) {
var c int
switch b {
case 'A', 'a':
c = 1
case 'C', 'c':
c = 2
case 'G', 'g':
c = 4
case 'T', 't', 'U', 'u':
c = 8
case 'N', 'n':
c = 15
case 'M', 'm':
c = 3
case 'R', 'r':
c = 5
case 'W', 'w':
c = 9
case 'S', 's':
c = 6
case 'Y', 'y':
c = 10
case 'K', 'k':
c = 12
case 'V', 'v':
c = 7
case 'H', 'h':
c = 11
case 'D', 'd':
c = 13
case 'B', 'b':
c = 14
case ' ', '*', '-':
c = 0
default:
return 0, ErrInvalidDNABase
}
return c, nil
}
// Bases2AmbBase converts list of bases to ambiguous base
func Bases2AmbBase(bs []byte) (byte, error) {
var code, c int
var err error
for _, b := range bs {
c, err = base2code(b)
if err != nil {
return 0, err
}
code |= c
}
return code2base[code], nil
}
// Codes2AmbCode converts list of codes of bases to code of ambiguous base
func Codes2AmbCode(codes []int) (int, error) {
var code int
for _, c := range codes {
code |= c
}
return code, nil
}
// AmbBase2Bases0 converts ambiguous base to bases it represents, slower than AmbBase2Bases
func AmbBase2Bases0(b byte) ([]byte, error) {
code, err := base2code(b)
if err != nil {
return nil, err
}
bases := []byte{}
var c int
for comb := 1; comb <= code; comb++ {
c = 0
for i := uint(0); i < 4; i++ {
if (comb>>i)&1 == 1 && // this combination needs this bit being 1
code&(1< 0 { // this bit is 1
c += 1 << i
}
}
if c == comb { // all bits are set
bases = append(bases, code2base[c])
}
}
return bases, nil
}
// AmbBase2Bases holds relationship of ambiguous base and bases it represents, faster than AmbBase2Bases0
var AmbBase2Bases = map[byte][]byte{
'A': {'A'},
'a': {'A'},
'C': {'C'},
'c': {'C'},
'G': {'G'},
'g': {'G'},
'T': {'T'},
't': {'T'},
'U': {'T'},
'u': {'T'},
'M': {'A', 'C', 'M'},
'm': {'A', 'C', 'M'},
'R': {'A', 'G', 'R'},
'r': {'A', 'G', 'R'},
'W': {'A', 'T', 'W'},
'w': {'A', 'T', 'W'},
'S': {'C', 'G', 'S'},
's': {'C', 'G', 'S'},
'Y': {'C', 'T', 'Y'},
'y': {'C', 'T', 'Y'},
'K': {'G', 'T', 'K'},
'k': {'G', 'T', 'K'},
'V': {'A', 'C', 'G', 'M', 'R', 'S', 'V'},
'v': {'A', 'C', 'G', 'M', 'R', 'S', 'V'},
'H': {'A', 'C', 'T', 'M', 'W', 'Y', 'H'},
'h': {'A', 'C', 'T', 'M', 'W', 'Y', 'H'},
'D': {'A', 'G', 'T', 'R', 'W', 'K', 'D'},
'd': {'A', 'G', 'T', 'R', 'W', 'K', 'D'},
'B': {'C', 'G', 'T', 'S', 'Y', 'K', 'B'},
'b': {'C', 'G', 'T', 'S', 'Y', 'K', 'B'},
'N': {'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'},
'n': {'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'},
}
// AmbCodes2Codes is code version of AmbBase2Bases
var AmbCodes2Codes = map[int][]int{
1: {1},
2: {2},
4: {4},
8: {8},
3: {1, 2, 3},
5: {1, 4, 5},
9: {1, 8, 9},
6: {2, 4, 6},
10: {2, 8, 10},
12: {4, 8, 12},
7: {1, 2, 4, 3, 5, 6, 7},
11: {1, 2, 8, 3, 9, 10, 11},
13: {1, 4, 8, 5, 9, 12, 13},
14: {2, 4, 8, 6, 10, 12, 14},
15: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15},
}
bio-0.13.3/seq/ambiguous_bases.tsv 0000664 0000000 0000000 00000000224 14573550650 0017055 0 ustar 00root root 0000000 0000000 base bases complement
A A T
C C G
G G C
T/U T A
M A/C K
R A/G Y
W A/T W
S C/G S
Y C/T R
K G/T M
V A/C/G B
H A/C/T D
D A/G/T H
B C/G/T V
N A/C/G/T N
bio-0.13.3/seq/ambiguous_bases_test.go 0000664 0000000 0000000 00000006430 14573550650 0017712 0 ustar 00root root 0000000 0000000 package seq
import (
"bytes"
"sort"
"testing"
"github.com/cznic/sortutil"
)
func TestBases2AmbBase(t *testing.T) {
type Test struct {
bases []byte
ambase byte
err error
}
tests := []Test{
{[]byte{'A'}, 'A', nil},
{[]byte{'c'}, 'C', nil},
{[]byte{'t'}, 'T', nil},
{[]byte{'u'}, 'T', nil},
{[]byte{'g'}, 'G', nil},
{[]byte{'a', 'c'}, 'M', nil},
{[]byte{'c', 'a'}, 'M', nil},
{[]byte{'a', 'g'}, 'R', nil},
{[]byte{'g', 'a'}, 'R', nil},
{[]byte{'a', 't'}, 'W', nil},
{[]byte{'t', 'a'}, 'W', nil},
{[]byte{'c', 'g'}, 'S', nil},
{[]byte{'g', 'c'}, 'S', nil},
{[]byte{'c', 't'}, 'Y', nil},
{[]byte{'t', 'c'}, 'Y', nil},
{[]byte{'g', 't'}, 'K', nil},
{[]byte{'t', 'g'}, 'K', nil},
{[]byte{'a', 'c', 'g'}, 'V', nil},
{[]byte{'a', 'c', 't'}, 'H', nil},
{[]byte{'a', 'G', 't'}, 'D', nil},
{[]byte{'C', 'g', 't'}, 'B', nil},
{[]byte{'C', 'g', 't', 'a'}, 'N', nil},
{[]byte{'j'}, 'N', ErrInvalidDNABase},
}
var amb byte
var err error
for _, test := range tests {
amb, err = Bases2AmbBase(test.bases)
if err != nil {
if err != ErrInvalidDNABase {
t.Errorf("error should be: %s, got: %s", ErrInvalidDNABase, err)
} else {
continue
}
}
if amb != test.ambase {
t.Errorf("Test Bases2AmbBase Err: %s, need: %c, got: %c\n", test.bases, test.ambase, amb)
}
}
}
type _AmbBase2BasesTest struct {
ambase byte
bases []byte
err error
}
var tests4AmbBase2Bases = []_AmbBase2BasesTest{
{'A', []byte{'A'}, nil},
{'C', []byte{'C'}, nil},
{'G', []byte{'G'}, nil},
{'T', []byte{'T'}, nil},
{'M', []byte{'A', 'C', 'M'}, nil},
{'R', []byte{'A', 'G', 'R'}, nil},
{'W', []byte{'A', 'T', 'W'}, nil},
{'S', []byte{'C', 'G', 'S'}, nil},
{'Y', []byte{'C', 'T', 'Y'}, nil},
{'K', []byte{'G', 'T', 'K'}, nil},
{'V', []byte{'A', 'C', 'G', 'M', 'R', 'S', 'V'}, nil},
{'H', []byte{'A', 'C', 'T', 'M', 'W', 'Y', 'H'}, nil},
{'D', []byte{'A', 'G', 'T', 'R', 'W', 'K', 'D'}, nil},
{'B', []byte{'C', 'G', 'T', 'S', 'Y', 'K', 'B'}, nil},
{'N', []byte{'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'}, nil},
}
func TestAmbBase2Bases(t *testing.T) {
var bases []byte
var err error
var b1, b2 sortutil.ByteSlice
for _, test := range tests4AmbBase2Bases {
bases, err = AmbBase2Bases0(test.ambase)
if err != nil {
if err != ErrInvalidDNABase {
t.Errorf("error should be: %s, got: %s", ErrInvalidDNABase, err)
} else {
continue
}
}
b1 = sortutil.ByteSlice(bases)
b2 = sortutil.ByteSlice(test.bases)
sort.Sort(b1)
sort.Sort(b2)
if !bytes.Equal(b1, b2) {
t.Errorf("Test AmbBase2Bases0 Err: %c, need: %s, got: %s\n", test.ambase, b2, b1)
}
}
}
var RESULT [][]byte
func BenchmarkAmbBase2Bases0(b *testing.B) {
for i := 0; i < b.N; i++ {
var err error
result := [][]byte{}
for _, test := range tests4AmbBase2Bases {
var bases []byte
bases, err = AmbBase2Bases0(test.ambase)
if err != nil {
b.Errorf("Bench AmbBase2Bases0 Err")
}
result = append(result, bases)
}
RESULT = result
}
}
func BenchmarkAmbBase2Bases(b *testing.B) {
for i := 0; i < b.N; i++ {
var ok bool
result := [][]byte{}
for _, test := range tests4AmbBase2Bases {
var bases []byte
if bases, ok = AmbBase2Bases[test.ambase]; ok {
result = append(result, bases)
}
}
RESULT = result
}
}
bio-0.13.3/seq/codon_table_standard.amb.tsv 0000664 0000000 0000000 00000000060 14573550650 0020572 0 ustar 00root root 0000000 0000000 ACN T
CCN P
CGN R
CTN L
GCN A
GGN G
GTN V
TCN S
bio-0.13.3/seq/codon_table_standard.tsv 0000664 0000000 0000000 00000001217 14573550650 0020041 0 ustar 00root root 0000000 0000000 b1 b2 b3 aa m
T T T F -
T T C F -
T T A L -
T T G L M
T C T S -
T C C S -
T C A S -
T C G S -
T A T Y -
T A C Y -
T A A * *
T A G * *
T G T C -
T G C C -
T G A * *
T G G W -
C T T L -
C T C L -
C T A L -
C T G L M
C C T P -
C C C P -
C C A P -
C C G P -
C A T H -
C A C H -
C A A Q -
C A G Q -
C G T R -
C G C R -
C G A R -
C G G R -
A T T I -
A T C I -
A T A I -
A T G M M
A C T T -
A C C T -
A C A T -
A C G T -
A A T N -
A A C N -
A A A K -
A A G K -
A G T S -
A G C S -
A G A R -
A G G R -
G T T V -
G T C V -
G T A V -
G T G V -
G C T A -
G C C A -
G C A A -
G C G A -
G A T D -
G A C D -
G A A E -
G A G E -
G G T G -
G G C G -
G G A G -
G G G G -
bio-0.13.3/seq/codon_tables.go 0000664 0000000 0000000 00000052000 14573550650 0016131 0 ustar 00root root 0000000 0000000 // https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes
package seq
import (
"bytes"
"errors"
"fmt"
"sort"
"strings"
)
// ErrInvalidCodon means the length of codon is not 3.
var ErrInvalidCodon = errors.New("seq: invalid codon")
// ErrUnknownCodon means the codon is not in the codon table, or the codon contains bases expcet for A C T G U.
var ErrUnknownCodon = errors.New("seq: unknown codon")
// CodonTable represents a codon table
type CodonTable struct {
ID int
Name string
InitCodons map[string]struct{} // upper-case of codon as string, map for fast quering
StopCodons map[string]struct{} // upper-case of codon as string, map for fast quering
table [16][16][16]byte // matrix is much faster than map for quering
}
// NewCodonTable contructs a CodonTable with ID and Name,
// you need to set the detailed codon table by calling Set or Set2.
func NewCodonTable(id int, name string) *CodonTable {
t := &CodonTable{ID: id, Name: name}
t.InitCodons = make(map[string]struct{}, 1)
t.StopCodons = make(map[string]struct{}, 1)
t.table = [16][16][16]byte{}
return t
}
// String returns details of the CodonTable.
func (t CodonTable) String() string {
return t.string(false)
}
// StringWithAmbiguousCodons returns details of the CodonTable， including ambiguous codons.
func (t CodonTable) StringWithAmbiguousCodons() string {
return t.string(true)
}
func (t CodonTable) string(showAmbiguousCodon bool) string {
var b bytes.Buffer
b.WriteString(fmt.Sprintf("%s (transl_table=%d)\n", t.Name, t.ID))
b.WriteString(fmt.Sprintf("Source: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG%d\n", t.ID))
b.WriteString("\nInitiation Codons:\n ")
codons := make([]string, len(t.InitCodons))
i := 0
for codon := range t.InitCodons {
codons[i] = codon
i++
}
sort.Strings(codons)
b.WriteString(strings.Join(codons, ", "))
b.WriteString("\n\nStop Codons:\n ")
codons = make([]string, len(t.StopCodons))
i = 0
for codon := range t.StopCodons {
codons[i] = codon
i++
}
sort.Strings(codons)
b.WriteString(strings.Join(codons, ", "))
b.WriteString("\n\nStranslate Table:\n")
var aa byte
var flag, flag2 bool
var buf []string
for i := 1; i < 16; i++ {
if !showAmbiguousCodon && i != 1 && i != 2 && i != 4 && i != 8 {
continue
}
flag2 = false
for j := 1; j < 16; j++ {
if !showAmbiguousCodon && (j != 1 && j != 2 && j != 4 && j != 8) {
continue
}
buf = make([]string, 0, 16)
flag = false
for k := 1; k < 16; k++ {
if !showAmbiguousCodon && k != 1 && k != 2 && k != 4 && k != 8 {
continue
}
aa = t.table[i][j][k]
if aa != 0 {
buf = append(buf, fmt.Sprintf("%c%c%c: %c", code2base[i], code2base[j], code2base[k], aa))
flag = true
flag2 = true
}
}
if flag {
b.WriteString(" " + strings.Join(buf, ", ") + "\n")
}
}
if flag2 {
b.WriteString("\n")
}
}
return b.String()
}
// codon2idx returns the location of a codon in the matrix.
func codon2idx(codon []byte) (int, int, int, error) {
if len(codon) != 3 {
return 0, 0, 0, ErrInvalidCodon
}
var err error
var i, j, k int
i, err = base2code(codon[0])
if err != nil {
return 0, 0, 0, err
}
j, err = base2code(codon[1])
if err != nil {
return 0, 0, 0, err
}
k, err = base2code(codon[2])
if err != nil {
return 0, 0, 0, err
}
return i, j, k, nil
}
// Set sets a codon of byte slice.
func (t *CodonTable) Set(codon []byte, aminoAcid byte) error {
i, j, k, err := codon2idx(codon)
if err != nil {
return err
}
t.table[i][j][k] = aminoAcid
return nil
}
// Set2 sets a codon of string.
func (t *CodonTable) Set2(codon string, aminoAcid byte) error {
return t.Set([]byte(codon), aminoAcid)
}
// Get returns the amino acid of the codon ([]byte), codon can be DNA or RNA.
// When allowUnknownCodon is true, codons that not int the codon table will
// still be translated to 'X', and "---" is translated to "-".
func (t *CodonTable) Get(codon []byte, allowUnknownCodon bool) (byte, error) {
i, j, k, err := codon2idx(codon)
if err != nil {
if allowUnknownCodon && err == ErrInvalidDNABase {
return 'X', nil
}
return 0, err
}
if codon[0] == '-' && codon[1] == '-' && codon[2] == '-' {
return '-', nil
}
aa := t.table[i][j][k]
if aa == 0 {
aa = 'X'
}
return aa, nil
}
// Get2 returns the amino acid of the codon (string), codon can be DNA or RNA.
func (t *CodonTable) Get2(codon string, allowUnknownCodon bool) (byte, error) {
return t.Get([]byte(codon), allowUnknownCodon)
}
// Clone returns a deep copy of the CodonTable.
func (t *CodonTable) Clone() CodonTable {
initCodons := make(map[string]struct{}, len(t.InitCodons))
for k, v := range t.InitCodons {
initCodons[k] = v
}
stopCodons := make(map[string]struct{}, len(t.StopCodons))
for k, v := range t.StopCodons {
stopCodons[k] = v
}
table := [16][16][16]byte{}
for i := 0; i < 16; i++ {
for j := 0; j < 16; j++ {
for k := 0; k < 16; k++ {
table[i][j][k] = t.table[i][j][k]
}
}
}
return CodonTable{ID: t.ID, Name: t.Name, InitCodons: initCodons, StopCodons: stopCodons, table: table}
}
// Translate translates a DNA/RNA sequence to amino acid sequences.
// Available frame: 1, 2, 3, -1, -2 ,-3.
// If option trim is true, it removes all 'X' and '*' characters from the right end of the translation.
// If option clean is true, it changes all STOP codon positions from the '*' character to 'X' (an unknown residue).
// If option allowUnknownCodon is true, codons not in the codon table will be translated to 'X'.
// If option markInitCodonAsM is true, initial codon at beginning will be represented as 'M'.
func (t *CodonTable) Translate(sequence []byte, frame int, trim bool, clean bool, allowUnknownCodon bool, markInitCodonAsM bool) ([]byte, error) {
if len(sequence) < 3 {
return nil, fmt.Errorf("seq: sequence too short to translate: %d", len(sequence))
}
if frame < -3 || frame > 3 || frame == 0 {
return nil, fmt.Errorf("seq: invalid frame: %d. available: 1, 2, 3, -1, -2, -3", frame)
}
aas := make([]byte, 0, int((len(sequence)+2)/3))
var aa byte
var err error
first := true
var ok bool
if frame < 0 {
l := len(sequence)
codon := make([]byte, 3)
rc := DNA.PairLetter
for i := l + frame; i >= 2; i -= 3 {
codon[0], _ = rc(sequence[i])
codon[1], _ = rc(sequence[i-1])
codon[2], _ = rc(sequence[i-2])
aa, err = t.Get(codon, allowUnknownCodon)
if err != nil {
return nil, err
}
if markInitCodonAsM {
if first {
// convert amino acid of start codon to 'M'
if _, ok = t.InitCodons[strings.ToUpper(string(codon))]; ok {
aa = 'M'
}
first = false
} else if aa == '*' {
first = true
}
}
if trim && (aa == 'X' || aa == '*') {
break
}
if clean && aa == '*' {
aa = 'X'
}
aas = append(aas, aa)
}
} else {
for i := frame - 1; i < len(sequence)-2; i += 3 {
aa, err = t.Get(sequence[i:i+3], allowUnknownCodon)
if err != nil {
return nil, err
}
if markInitCodonAsM {
if first {
// convert amino acid of start codon to 'M'
_, ok = t.InitCodons[strings.ToUpper(string(sequence[i:i+3]))]
if ok {
aa = 'M'
}
first = false
} else if aa == '*' {
first = true
}
}
if trim && (aa == 'X' || aa == '*') {
break
}
if clean && aa == '*' {
aa = 'X'
}
aas = append(aas, aa)
}
}
return aas, nil
}
// CodonTables contains all the codon tables from NCBI:
//
// 1: The Standard Code
// 2: The Vertebrate Mitochondrial Code
// 3: The Yeast Mitochondrial Code
// 4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
// 5: The Invertebrate Mitochondrial Code
// 6: The Ciliate, Dasycladacean and Hexamita Nuclear Code
// 9: The Echinoderm and Flatworm Mitochondrial Code
// 10: The Euplotid Nuclear Code
// 11: The Bacterial, Archaeal and Plant Plastid Code
// 12: The Alternative Yeast Nuclear Code
// 13: The Ascidian Mitochondrial Code
// 14: The Alternative Flatworm Mitochondrial Code
// 16: Chlorophycean Mitochondrial Code
// 21: Trematode Mitochondrial Code
// 22: Scenedesmus obliquus Mitochondrial Code
// 23: Thraustochytrium Mitochondrial Code
// 24: Pterobranchia Mitochondrial Code
// 25: Candidate Division SR1 and Gracilibacteria Code
// 26: Pachysolen tannophilus Nuclear Code
// 27: Karyorelict Nuclear
// 28: Condylostoma Nuclear
// 29: Mesodinium Nuclear
// 30: Peritrich Nuclear
// 31: Blastocrithidia Nuclear
//
var CodonTables map[int]*CodonTable
// https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG1
func codonTableFromText(id int, name string, text string) *CodonTable {
t := NewCodonTable(id, name)
data := strings.Split(text, "\n")
if !(len(data) == 5 && len(data[0]) == 64 && len(data[1]) == 64 &&
len(data[2]) == 64 && len(data[3]) == 64 && len(data[4]) == 64) {
panic("please paste the right text from NCBI")
}
var aa, start byte
var codon []byte
for i := 0; i < 64; i++ {
aa = data[0][i]
start = data[1][i]
codon = []byte{data[2][i], data[3][i], data[4][i]}
t.Set(codon, aa)
if start == 'M' {
t.InitCodons[strings.ToUpper(string(codon))] = struct{}{}
} else if start == '*' {
t.StopCodons[strings.ToUpper(string(codon))] = struct{}{}
}
}
// supporting codon containing ambiguous base
var m map[byte][]int // aa - > bases
var ok bool
var codes, ambcodes []int
var code, ambcode int
// base3
for i := 1; i < 16; i++ {
for j := 1; j < 16; j++ {
m = make(map[byte][]int, 16)
for k := 1; k < 16; k++ {
aa = t.table[i][j][k]
if aa == 0 {
continue
}
if _, ok = m[aa]; !ok {
m[aa] = make([]int, 0, 4)
}
m[aa] = append(m[aa], k)
}
if len(m) == 0 {
continue
}
for aa, codes = range m {
ambcode, _ = Codes2AmbCode(codes)
if ambcodes, ok = AmbCodes2Codes[ambcode]; ok {
for _, code = range ambcodes {
t.table[i][j][code] = aa
}
}
}
}
}
// base2
for i := 1; i < 16; i++ {
for k := 1; k < 16; k++ {
m = make(map[byte][]int, 16)
for j := 1; j < 16; j++ {
aa = t.table[i][j][k]
if aa == 0 {
continue
}
if _, ok = m[aa]; !ok {
m[aa] = make([]int, 0, 4)
}
m[aa] = append(m[aa], j)
}
if len(m) == 0 {
continue
}
for aa, codes = range m {
ambcode, _ = Codes2AmbCode(codes)
if ambcodes, ok = AmbCodes2Codes[ambcode]; ok {
for _, code = range ambcodes {
t.table[i][code][k] = aa
}
}
}
}
}
// base1
for j := 1; j < 16; j++ {
for k := 1; k < 16; k++ {
m = make(map[byte][]int, 16)
for i := 1; i < 16; i++ {
aa = t.table[i][j][k]
if aa == 0 {
continue
}
if _, ok = m[aa]; !ok {
m[aa] = make([]int, 0, 4)
}
m[aa] = append(m[aa], i)
}
if len(m) == 0 {
continue
}
for aa, codes = range m {
ambcode, _ = Codes2AmbCode(codes)
if ambcodes, ok = AmbCodes2Codes[ambcode]; ok {
for _, code = range ambcodes {
t.table[code][j][k] = aa
}
}
}
}
}
return t
}
func init() {
CodonTables = make(map[int]*CodonTable, 31)
CodonTables[1] = codonTableFromText(1,
"The Standard Code",
`FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
---M------**--*----M---------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[2] = codonTableFromText(2,
"The Vertebrate Mitochondrial Code",
`FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
----------**--------------------MMMM----------**---M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[3] = codonTableFromText(3,
"The Yeast Mitochondrial Code",
`FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
----------**----------------------MM----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[4] = codonTableFromText(4,
"The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code",
`FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
--MM------**-------M------------MMMM---------------M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[5] = codonTableFromText(5,
"The Invertebrate Mitochondrial Code ",
`FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
---M------**--------------------MMMM---------------M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[6] = codonTableFromText(6,
"The Ciliate, Dasycladacean and Hexamita Nuclear Code",
`FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
--------------*--------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[9] = codonTableFromText(9,
"The Echinoderm and Flatworm Mitochondrial Code",
`FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
----------**-----------------------M---------------M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[10] = codonTableFromText(10,
"The Euplotid Nuclear Code",
`FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
----------**-----------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[11] = codonTableFromText(11,
"The Bacterial, Archaeal and Plant Plastid Code",
`FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
---M------**--*----M------------MMMM---------------M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[12] = codonTableFromText(12,
"The Alternative Yeast Nuclear Code",
`FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
----------**--*----M---------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[13] = codonTableFromText(13,
"The Ascidian Mitochondrial Code",
`FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
---M------**----------------------MM---------------M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[14] = codonTableFromText(14,
"The Alternative Flatworm Mitochondrial Code",
`FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
-----------*-----------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[16] = codonTableFromText(16,
"Chlorophycean Mitochondrial Code",
`FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
----------*---*--------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[21] = codonTableFromText(21,
"Trematode Mitochondrial Code",
`FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
----------**-----------------------M---------------M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[22] = codonTableFromText(22,
"Scenedesmus obliquus Mitochondrial Code",
`FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
------*---*---*--------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[23] = codonTableFromText(23,
"Thraustochytrium Mitochondrial Code",
`FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
--*-------**--*-----------------M--M---------------M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[24] = codonTableFromText(24,
"Pterobranchia Mitochondrial Code",
`FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG
---M------**-------M---------------M---------------M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[25] = codonTableFromText(25,
"Candidate Division SR1 and Gracilibacteria Code",
`FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
---M------**-----------------------M---------------M------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[26] = codonTableFromText(26,
"Pachysolen tannophilus Nuclear Code",
`FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
----------**--*----M---------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[27] = codonTableFromText(27,
"Karyorelict Nuclear",
`FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
--------------*--------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[28] = codonTableFromText(28,
"Condylostoma Nuclear",
`FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
----------**--*--------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[29] = codonTableFromText(29,
"Mesodinium Nuclear",
`FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
--------------*--------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[30] = codonTableFromText(30,
"Peritrich Nuclear",
`FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
--------------*--------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
CodonTables[31] = codonTableFromText(31,
"Blastocrithidia Nuclear",
`FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
----------**-----------------------M----------------------------
TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG`)
// ks := make([]int, len(CodonTables))
// i := 0
// for k := range CodonTables {
// ks[i] = k
// i++
// }
// sort.Ints(ks)
// for _, i = range ks {
// fmt.Println(CodonTables[i])
// // fmt.Printf("%d: %s\n", CodonTables[i].ID, CodonTables[i].Name)
// break
// }
}
bio-0.13.3/seq/codon_tables_test.go 0000664 0000000 0000000 00000012407 14573550650 0017177 0 ustar 00root root 0000000 0000000 package seq
import (
"regexp"
"testing"
)
type codonTableTest struct {
table int
nt string
aa string
frame int
trim bool
clean bool
allowUnknownCodon bool
markInitCodonAsM bool
}
var codonTableTests []codonTableTest
func init() {
re := regexp.MustCompile(`\r?\n|\s`)
codonTableTests = make([]codonTableTest, 0, 10)
// https://www.ncbi.nlm.nih.gov/nuccore/AB021961.1
codonTableTests = append(codonTableTests,
codonTableTest{
table: 1,
nt: re.ReplaceAllString(`atgactgccatggaggagtcacagtcggatatcagcctcgagctccctctgagccaggag
acattttcaggcttatggaaactacttcctccagaagatatcctgccatcacctcactgc
atggacgatctgttgctgccccaggatgttgaggagttttttgaaggcccaagtgaagcc
ctccgagtgtcaggagctcctgcagcacaggaccctgtcaccgagacccctgggccagtg
gcccctgccccagccactccatggcccctgtcatcttttgtcccttctcaaaaaacttac
cagggcaactatggcttccacctgggcttcctgcagtctgggacagccaagtctgttatg
tgcacgtactctcctcccctcaataagctattctgccagctggcgaagacgtgccctgtg
cagttgtgggtcagcgccacacctccagctgggagccgtgtccgcgccatggccatctac
aagaagtcacagcacatgacggaggtcgtgagacgctgcccccaccatgagcgctgctcc
gatggtgatggcctggctcctccccagcatcgtatccgggtggaaggaaatttgtatccc
gagtatctggaagacaggcagacttttcgccacagcgtggtggtaccttatgagccaccc
gaggccggctctgagtataccaccatccactacaagtacatgtgtaatagctcctgcatg
gggggcatgaaccgccgacctatccttaccatcatcacactggaagactccagtgggaac
cttctgggacgggacagctttgaggttcgtgtttgtgcctgccctgggagagaccgccgt
acagaagaagaaaatttccgcaaaaaggaagtcctttgccctgaactgcccccagggagc
gcaaagagagcgctgcccacctgcacaagcgcctctcccccgcaaaagaaaaaaccactt
gatggagagtatttcaccctcaagatccgcgggcgtaaacgcttcgagatgttccgggag
ctgaatgaggccttagagttaaaggatgcccatgctacagaggagtctggagacagcagg
gctcactccagctacctgaagaccaagaagggccagtctacttcccgccataaaaaaaca
atggtcaagaaagtggggcctgactcagactga`, ""),
aa: re.ReplaceAllString(`MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDL
LLPQDVEEFFEGPSEALRVSGAPAAQDPVTETPGPVAPAPATPWPLSSFVPSQKTYQG
NYGFHLGFLQSGTAKSVMCTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIY
KKSQHMTEVVRRCPHHERCSDGDGLAPPQHRIRVEGNLYPEYLEDRQTFRHSVVVPYE
PPEAGSEYTTIHYKYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPG
RDRRTEEENFRKKEVLCPELPPGSAKRALPTCTSASPPQKKKPLDGEYFTLKIRGRKR
FEMFRELNEALELKDAHATEESGDSRAHSSYLKTKKGQSTSRHKKTMVKKVGPDSD`, ""),
frame: 1,
trim: true,
clean: false,
})
// ORF25 from https://www.ncbi.nlm.nih.gov/nuccore/AJ245616.1
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`atggaggaacaagcatggcgagaagtcctcgaacgtttagctcga
attgaaacaaagttagataactatgaaacagttcgagataaagcagaacgagcgctccta
atagctcaatcaaatgcgaaacttatagaaaaaatggaagctaataataagtgggcttgg
ggctttatgcttactcttgccgtaactgttattggttatttattcactaaaattagattc
tga`, ""),
aa: re.ReplaceAllString(`MEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF`, ""),
frame: 1,
trim: true,
clean: false,
})
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`tcagaatctaattttagtgaataaataaccaataacagttacggcaagagtaagcataaa
gccccaagcccacttattattagcttccattttttctataagtttcgcatttgattgagc
tattaggagcgctcgttctgctttatctcgaactgtttcatagttatctaactttgtttc
aattcgagctaaacgttcgaggacttctcgccatgcttgttcctccat`, ""),
aa: re.ReplaceAllString(`MEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF`, ""),
frame: -1,
trim: true,
clean: false,
})
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`tcagaatctaattttagtgaataaataaccaataacagttacggcaagagtaagcataaa
gccccaagcccacttattattagcttccattttttctataagtttcgcatttgattgagc
tattaggagcgctcgttctgctttatctcgaactgtttcatagttatctaactttgtttc
aattcgagctaaacgttcgaggacttctcgccatgcttgttcctccatc`, ""),
aa: re.ReplaceAllString(`MEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF`, ""),
frame: -2,
trim: true,
clean: false,
})
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`tcagaatctaattttagtgaataaataaccaataacagttacggcaagagtaagcataaa
gccccaagcccacttattattagcttccattttttctataagtttcgcatttgattgagc
tattaggagcgctcgttctgctttatctcgaactgtttcatagttatctaactttgtttc
aattcgagctaaacgttcgaggacttctcgccatgcttgttcctccatcc`, ""),
aa: re.ReplaceAllString(`MEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF`, ""),
frame: -3,
trim: true,
clean: false,
})
codonTableTests = append(codonTableTests,
codonTableTest{
table: 11,
nt: re.ReplaceAllString(`atNgaggaacaagcatggcgagaagtcctcgaacgtttagctcga
attgaaacaaagttagataactatgaaacagttcgagataaagcagaacgagcgctccta
atagctcaatcaaatgcgaaacttatagaaaaaatggaagctaataataagtgggcttgg
ggctttatgcttactcttgccgtaactgttattggttatttattcactaaaattagattc
tga`, ""),
aa: re.ReplaceAllString(`XEEQAWREVLERLARIETKLDNYETVRDKAERALLIAQSNAKLI
EKMEANNKWAWGFMLTLAVTVIGYLFTKIRF*`, ""),
frame: 1,
trim: false,
clean: false,
allowUnknownCodon: true,
})
}
func TestCodonTableStranslation(t *testing.T) {
var aa []byte
var err error
for i, test := range codonTableTests {
aa, err = CodonTables[test.table].Translate([]byte(test.nt), test.frame, test.trim, test.clean, test.allowUnknownCodon, test.markInitCodonAsM)
if err != nil {
t.Errorf("test %d err: %s", i, err)
}
if len(aa) != len(test.aa) {
t.Errorf("test %d err: len unequal, answer: %d, result: %d", i, len(aa), len(test.aa))
}
if string(aa) != test.aa {
t.Errorf("test %d err: result not right", i)
}
}
}
bio-0.13.3/seq/qual.go 0000775 0000000 0000000 00000014402 14573550650 0014446 0 ustar 00root root 0000000 0000000 package seq
import (
"errors"
"math"
"github.com/shenwei356/util/byteutil"
)
// ErrInvalidPhredQuality occurs for phred quality less than 0.
var ErrInvalidPhredQuality = errors.New("seq: invalid Phred quality")
// ErrInvalidSolexaQuality occurs for solexa quality less than -5.
var ErrInvalidSolexaQuality = errors.New("seq: invalid Solexa quality")
// Phred2Solexa converts Phred quality to Solexa quality.
func Phred2Solexa(q float64) (float64, error) {
if q == 0 {
return -5, nil
}
if q < 0 {
return -5, ErrInvalidPhredQuality
}
return max(-5, 10*math.Log10(math.Pow(10, q/10)-1)), nil
}
// Solexa2Phred converts Solexa quality to Phred quality.
func Solexa2Phred(q float64) (float64, error) {
if q < -5 {
return 0, ErrInvalidSolexaQuality
}
return 10 * math.Log10(math.Pow(10, q/10)+1), nil
}
func max(a float64, b float64) float64 {
if a > b {
return a
}
return b
}
// QualityEncoding is the type of quality encoding
type QualityEncoding int
// NQualityEncoding is the number of QualityEncoding + 1: 5 + 1 = 6
const NQualityEncoding int = 6
const (
// Unknown quality encoding
Unknown QualityEncoding = iota
// Sanger format can encode a Phred quality score from 0 to 93 using
// ASCII 33 to 126 (although in raw read data the Phred quality score
// rarely exceeds 60, higher scores are possible in assemblies or read maps).
Sanger
// Solexa /Illumina 1.0 format can encode a Solexa/Illumina quality score
// from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa
// scores from -5 to 40 only are expected).
Solexa
// Illumina1p3 means Illumina 1.3+.
// Starting with Illumina 1.3 and before Illumina 1.8, the format
// encoded a Phred quality score from 0 to 62 using ASCII 64 to 126
// (although in raw read data Phred scores from 0 to 40 only are expected).
Illumina1p3
// Illumina1p5 means Illumina 1.5+.
// Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores
// 0 to 2 have a slightly different meaning. The values 0 and 1 are
// no longer used and the value 2, encoded by ASCII 66 "B", is used
// also at the end of reads as a Read Segment Quality Control Indicator.
Illumina1p5
// Illumina1p8 means Illumina 1.8+.
// Starting in Illumina 1.8, the quality scores have basically
// returned to the use of the Sanger format (Phred+33)
Illumina1p8
)
func (qe QualityEncoding) String() string {
switch qe {
case Sanger:
return "Sanger"
case Solexa:
return "Solexa"
case Illumina1p3:
return "Illumina-1.3+"
case Illumina1p5:
return "Illumina-1.5+"
case Illumina1p8:
return "Illumina-1.8+"
}
return "Unknown"
}
// QualityRange is the typical quality range
func (qe QualityEncoding) QualityRange() []int {
switch qe {
case Sanger:
return []int{33, 126}
case Solexa:
return []int{59, 126}
case Illumina1p3:
return []int{64, 126}
case Illumina1p5:
return []int{66, 126}
case Illumina1p8:
return []int{33, 126}
}
return []int{127, 256}
}
// Offset is the ASCII offset
func (qe QualityEncoding) Offset() int {
switch qe {
case Sanger:
return 33
case Solexa:
return 64
case Illumina1p3:
return 64
case Illumina1p5:
return 64
case Illumina1p8:
return 33
}
return 0
}
// IsSolexa tells whether the encoding is Solexa
func (qe QualityEncoding) IsSolexa() bool {
switch qe {
case Solexa:
return true
}
return false
}
// ErrUnknownQualityEncoding is error for Unknown quality encoding type
var ErrUnknownQualityEncoding = errors.New("unknown quality encoding")
// QualityValue returns quality value for given encoding and quality string
func QualityValue(encoding QualityEncoding, quality []byte) ([]int, error) {
offset := encoding.Offset()
if offset == 0 {
return nil, ErrUnknownQualityEncoding
}
qv := make([]int, len(quality))
for i, q := range quality {
qv[i] = int(q) - offset
}
return qv, nil
}
// QualityConvert convert quality from one encoding to another encoding.
// Force means forcely truncate scores > 40 to 40 when converting Illumina-1.8+
// to Sanger.
func QualityConvert(from, to QualityEncoding, quality []byte, force bool) ([]byte, error) {
if from == to || from == Unknown || to == Unknown {
return quality, nil
}
qv, _ := QualityValue(from, quality)
isSolexaFrom := from.IsSolexa()
isSolexaTo := to.IsSolexa()
offsetTo := to.Offset()
var err error
var q2 float64
qualityNew := make([]byte, len(quality))
for i, q := range qv {
if force { // Illumina -> Sanger
if from == Illumina1p8 && to == Sanger && q > 40 {
q = 40
}
}
if from == Illumina1p5 && q == 2 { // special case of Illumina 1.5
q = 0
}
if isSolexaFrom == isSolexaTo {
qualityNew[i] = byte(q + offsetTo)
} else if isSolexaFrom {
q2, err = Solexa2Phred(float64(q))
if err != nil {
return nil, err
}
qualityNew[i] = byte(int(q2) + offsetTo)
} else {
q2, err = Phred2Solexa(float64(q))
if err != nil {
return nil, err
}
qualityNew[i] = byte(int(q2) + offsetTo)
}
}
return qualityNew, nil
}
// NMostCommonThreshold is the threshold of 'B' in
// top N most common quality for guessing Illumina 1.5.
var NMostCommonThreshold = 2
// GuessQualityEncoding returns potential quality encodings.
func GuessQualityEncoding(quality []byte) []QualityEncoding {
var encodings []QualityEncoding
min, max := qualRange(quality)
var encoding QualityEncoding
var r []int
var count map[byte]int
var countSorted byteutil.ByteCountList
var BEnriched bool
for i := 1; i < NQualityEncoding; i++ {
encoding = QualityEncoding(i)
r = encoding.QualityRange()
if min >= r[0] && max <= r[1] {
if encoding == Illumina1p5 {
if count == nil {
count = byteutil.CountOfByte(quality)
}
if count['@'] > 0 || count['A'] > 0 { // exclude Illumina 1.5
continue
} else { //
countSorted = byteutil.SortCountOfByte(count, true)
BEnriched = false
for i := 0; i < len(countSorted) && i < NMostCommonThreshold; i++ {
if countSorted[i].Key == 'B' {
BEnriched = true
break
}
}
if BEnriched {
return []QualityEncoding{Illumina1p5}
}
}
}
encodings = append(encodings, encoding)
}
}
return encodings
}
func qualRange(quality []byte) (int, int) {
var min, max int = 126, 0
var v int
for _, q := range quality {
v = int(q)
if v > max {
max = v
}
if v < min {
min = v
}
}
return min, max
}
bio-0.13.3/seq/qual_test.go 0000775 0000000 0000000 00000000554 14573550650 0015510 0 ustar 00root root 0000000 0000000 package seq
import (
"math"
"testing"
)
func TestPhredAndSolexa(t *testing.T) {
var q2, q3 float64
var err error
for q := 2.0; q <= 40; q++ {
q2, err = Phred2Solexa(q)
if err != nil {
t.Error(err)
}
q3, err = Solexa2Phred(q2)
if err != nil {
t.Error(err)
}
if math.Abs(q3-q) > 0.01 {
t.Errorf("%.2f, %.2f, %.2f", q, q2, q3)
}
}
}
bio-0.13.3/seq/seq.go 0000664 0000000 0000000 00000041214 14573550650 0014272 0 ustar 00root root 0000000 0000000 package seq
import (
"bytes"
"fmt"
"math"
"runtime"
"strings"
"sync"
"github.com/shenwei356/util/byteutil"
)
var QUAL_MAP [256]float64
func initQualMap() {
for i := range QUAL_MAP {
QUAL_MAP[i] = math.Pow(10, float64(i)/-10)
}
QUAL_MAP[255] = 1.0
}
func init() {
initQualMap()
}
// Seq represents a FASTA/Q record
type Seq struct {
Alphabet *Alphabet
Seq []byte
Qual []byte
QualValue []int
}
// ValidateSeq decides whether check sequence or not
var ValidateSeq = true
// NewSeq is constructor for type *Seq*
func NewSeq(t *Alphabet, s []byte) (*Seq, error) {
if ValidateSeq {
// check sequene first
if err := t.IsValid(s); err != nil {
return nil, err
}
}
seq := &Seq{Alphabet: t, Seq: s}
return seq, nil
}
// NewSeqWithQual is used to store fastq sequence
func NewSeqWithQual(t *Alphabet, s []byte, q []byte) (*Seq, error) {
if len(s) != len(q) {
return nil, fmt.Errorf("seq: unmatched length of sequence (%d) and quality (%d)", len(s), len(q))
}
seq, err := NewSeq(t, s)
if err != nil {
return nil, err
}
seq.Qual = q
return seq, nil
}
// NewSeqWithoutValidation create Seq without check the sequences
func NewSeqWithoutValidation(t *Alphabet, s []byte) (*Seq, error) {
seq := &Seq{Alphabet: t, Seq: s}
return seq, nil
}
// NewSeqWithQualWithoutValidation create Seq with quality without check the sequences
func NewSeqWithQualWithoutValidation(t *Alphabet, s []byte, q []byte) (*Seq, error) {
if len(s) != len(q) {
return nil, fmt.Errorf("seq: unmatched length of sequence (%d) and quality (%d)", len(s), len(q))
}
seq := &Seq{Alphabet: t, Seq: s, Qual: q}
return seq, nil
}
// Length returns the length of sequence
func (seq *Seq) Length() int {
return len(seq.Seq)
}
func (seq *Seq) String() string {
return fmt.Sprintf("%s, len:%d, seq:%s, qual:%s", seq.Alphabet.String(), len(seq.Seq), seq.Seq, seq.Qual)
}
// Clone of a Seq
func (seq *Seq) Clone() *Seq {
s := make([]byte, len(seq.Seq))
copy(s, seq.Seq)
q := make([]byte, len(seq.Qual))
copy(q, seq.Qual)
qv := make([]int, len(seq.QualValue))
copy(qv, seq.QualValue)
return &Seq{
Alphabet: seq.Alphabet.Clone(),
Seq: s,
Qual: q,
QualValue: qv,
}
}
// Clone2 clones the sequence except the alphabet
func (seq *Seq) Clone2() *Seq {
s := make([]byte, len(seq.Seq))
copy(s, seq.Seq)
q := make([]byte, len(seq.Qual))
copy(q, seq.Qual)
qv := make([]int, len(seq.QualValue))
copy(qv, seq.QualValue)
return &Seq{
Alphabet: seq.Alphabet,
Seq: s,
Qual: q,
QualValue: qv,
}
}
/*
SubSeq returns a sub seq. start and end is 1-based.
Examples:
1-based index 1 2 3 4 5 6 7 8 9 10
negative index 0-9-8-7-6-5-4-3-2-1
seq A C G T N a c g t n
1:1 A
2:4 C G T
-4:-2 c g t
-4:-1 c g t n
-1:-1 n
2:-2 C G T N a c g t
1:-1 A C G T N a c g t n
1:12 A C G T N a c g t n
-12:-1 A C G T N a c g t n
*/
func (seq *Seq) SubSeq(start int, end int) *Seq {
var newseq *Seq
start, end, ok := SubLocation(len(seq.Seq), start, end)
if ok {
s := make([]byte, end-start+1)
copy(s, seq.Seq[start-1:end])
newseq, _ = NewSeqWithoutValidation(seq.Alphabet, s)
if len(seq.Qual) > 0 {
newseq.Qual = []byte(string(seq.Qual[start-1 : end]))
}
if len(seq.QualValue) > 0 {
qv := make([]int, end-start+1)
for i, v := range seq.QualValue[start-1 : end] {
qv[i] = v
}
newseq.QualValue = qv
}
} else {
newseq, _ = NewSeqWithoutValidation(seq.Alphabet, []byte(""))
}
return newseq
}
// SubSeqInplace return subseq inplace
func (seq *Seq) SubSeqInplace(start int, end int) *Seq {
start, end, ok := SubLocation(len(seq.Seq), start, end)
if ok {
if len(seq.Seq) > 0 {
seq.Seq = seq.Seq[start-1 : end]
}
if len(seq.Qual) > 0 {
seq.Qual = seq.Qual[start-1 : end]
}
if len(seq.QualValue) > 0 {
seq.QualValue = seq.QualValue[start-1 : end]
}
} else {
seq.Seq = []byte{}
seq.Qual = []byte{}
seq.QualValue = []int{}
}
return seq
}
/*
SubLocation is my sublocation strategy,
start, end and returned start and end are all 1-based
1-based index 1 2 3 4 5 6 7 8 9 10
negative index 0-9-8-7-6-5-4-3-2-1
seq A C G T N a c g t n
1:1 A
2:4 C G T
-4:-2 c g t
-4:-1 c g t n
-1:-1 n
2:-2 C G T N a c g t
1:-1 A C G T N a c g t n
1:12 A C G T N a c g t n
-12:-1 A C G T N a c g t n
*/
func SubLocation(length, start, end int) (int, int, bool) {
if length == 0 {
return 0, 0, false
}
if start < 1 {
if start == 0 {
start = 1
} else if start < 0 {
if end < 0 && start > end {
return start, end, false
}
if -start > length {
return start, end, false
}
start = length + start + 1
}
}
if start > length {
return start, end, false
}
if end > length {
end = length
}
if end < 1 {
if end == 0 {
end = -1
}
end = length + end + 1
}
if start-1 > end {
return start - 1, end, false
}
return start, end, true
}
// RemoveGaps return a new seq without gaps
func (seq *Seq) RemoveGaps(letters string) *Seq {
if len(letters) == 0 {
return seq.Clone()
}
// do not use map
querySlice := make([]byte, 256)
for i := 0; i < len(letters); i++ {
querySlice[int(letters[i])] = letters[i]
}
s := make([]byte, len(seq.Seq))
q := make([]byte, len(seq.Qual))
var b, g byte
var j int
for i := 0; i < len(seq.Seq); i++ {
b = seq.Seq[i]
g = querySlice[int(b)]
if g == 0 { // not gap
s[j] = b
if len(seq.Qual) > 0 {
q[j] = seq.Qual[i]
}
j++
}
}
var newSeq *Seq
if len(seq.Qual) > 0 {
newSeq, _ = NewSeqWithQualWithoutValidation(seq.Alphabet, s[0:j], q[0:j])
} else {
newSeq, _ = NewSeqWithoutValidation(seq.Alphabet, s[0:j])
}
return newSeq
}
// RemoveGapsInplace removes gaps in place
func (seq *Seq) RemoveGapsInplace(letters string) *Seq {
if len(letters) == 0 {
return seq
}
// do not use map
querySlice := make([]byte, 256)
for i := 0; i < len(letters); i++ {
querySlice[int(letters[i])] = letters[i]
}
s := make([]byte, len(seq.Seq))
q := make([]byte, len(seq.Qual))
var b, g byte
var j int
for i := 0; i < len(seq.Seq); i++ {
b = seq.Seq[i]
g = querySlice[int(b)]
if g == 0 { // not gap
s[j] = b
if len(seq.Qual) > 0 {
q[j] = seq.Qual[i]
}
j++
}
}
seq.Seq = s[0:j]
if len(seq.Qual) > 0 {
seq.Qual = q[0:j]
}
return seq
}
// Bases counts non-gap bases
func (seq *Seq) Bases(gapLetters string) int {
if len(gapLetters) == 0 {
return seq.Length()
}
// do not use map
querySlice := make([]byte, 256)
for i := 0; i < len(gapLetters); i++ {
querySlice[int(gapLetters[i])] = gapLetters[i]
}
var n int
for i := 0; i < len(seq.Seq); i++ {
if querySlice[int(seq.Seq[i])] == 0 { // not gap
n++
}
}
return n
}
// RevCom returns reverse complement sequence
func (seq *Seq) RevCom() *Seq {
return seq.Reverse().Complement()
}
// RevComInplace reverses complement sequence in place
func (seq *Seq) RevComInplace() *Seq {
return seq.ReverseInplace().ComplementInplace()
}
// Reverse a sequence
func (seq *Seq) Reverse() *Seq {
return seq.Clone().ReverseInplace()
}
// ReverseInplace reverses the sequence content
func (seq *Seq) ReverseInplace() *Seq {
if len(seq.Qual) > 0 {
byteutil.ReverseByteSliceInplace(seq.Qual)
}
byteutil.ReverseByteSliceInplace(seq.Seq)
return seq
}
// ComplementSeqLenThreshold is the threshold of sequence length that
// needed to parallelly complement sequence
var ComplementSeqLenThreshold = 1000000
// ComplementThreads is the threads number of parallelly complement sequence
var ComplementThreads = runtime.NumCPU()
// Complement returns complement sequence.
func (seq *Seq) Complement() *Seq {
return seq.Clone().ComplementInplace()
}
// ComplementInplace returns complement sequence.
func (seq *Seq) ComplementInplace() *Seq {
if seq.Alphabet == Unlimit {
return seq
}
l := len(seq.Seq)
if l < ComplementSeqLenThreshold {
var p byte
for i := 0; i < len(seq.Seq); i++ {
p, _ = seq.Alphabet.PairLetter(seq.Seq[i])
seq.Seq[i] = p
}
return seq
}
chunkSize, start, end := int(l/ComplementThreads), 0, 0
var wg sync.WaitGroup
tokens := make(chan int, ComplementThreads)
for i := 0; i < ComplementThreads; i++ {
start = i * chunkSize
end = (i + 1) * chunkSize
if i == ComplementThreads-1 && end < l {
end = l
}
if end > l {
end = l
}
tokens <- 1
wg.Add(1)
go func(alphabet *Alphabet, start, end int) {
var p byte
for i := start; i < end; i++ {
p, _ = seq.Alphabet.PairLetter(seq.Seq[i])
seq.Seq[i] = p
}
<-tokens
wg.Done()
}(seq.Alphabet, start, end)
}
wg.Wait()
return seq
}
// FormatSeq wrap seq
func (seq *Seq) FormatSeq(width int) []byte {
return byteutil.WrapByteSlice(seq.Seq, width)
}
/*
BaseContent returns base content for given bases. For example:
seq.BaseContent("gc")
*/
func (seq *Seq) BaseContent(list string) float64 {
if len(seq.Seq) == 0 {
return float64(0)
}
return float64(seq.BaseCount(list)) / float64(len(seq.Seq))
}
// BaseCount counts bases
func (seq *Seq) BaseCount(list string) int {
if len(seq.Seq) == 0 {
return 0
}
sum := 0
for _, b := range []byte(list) {
up := bytes.ToUpper([]byte{b})
lo := bytes.ToLower([]byte{b})
if string(up) == string(lo) {
sum += bytes.Count(seq.Seq, up)
} else {
sum += bytes.Count(seq.Seq, up) + bytes.Count(seq.Seq, lo)
}
}
return sum
}
// BaseContentCaseSensitive returns base content for given case sensitive bases.
func (seq *Seq) BaseContentCaseSensitive(list string) float64 {
if len(seq.Seq) == 0 {
return float64(0)
}
return float64(seq.BaseCountCaseSensitive(list)) / float64(len(seq.Seq))
}
// BaseCountCaseSensitive counts bases, case is not ignored.
func (seq *Seq) BaseCountCaseSensitive(list string) int {
if len(seq.Seq) == 0 {
return 0
}
sum := 0
for _, b := range []byte(list) {
sum += bytes.Count(seq.Seq, []byte{b})
}
return sum
}
// GC returns the GC content
func (seq *Seq) GC() float64 {
return seq.BaseContent("gcs")
}
// DegenerateBaseMapNucl mappings nucleic acid degenerate base to
// regular expression
var DegenerateBaseMapNucl = map[byte]string{
'A': "A",
'T': "[TU]",
'U': "[TU]",
'C': "C",
'G': "G",
'R': "[AG]",
'Y': "[CTU]",
'M': "[AC]",
'K': "[GTU]",
'S': "[CG]",
'W': "[ATU]",
'H': "[ACTU]",
'B': "[CGTU]",
'V': "[ACG]",
'D': "[AGTU]",
'N': "[ACGTU]",
'a': "a",
't': "[tu]",
'u': "[tu]",
'c': "c",
'g': "g",
'r': "[ag]",
'y': "[ctu]",
'm': "[ac]",
'k': "[gtu]",
's': "[cg]",
'w': "[atu]",
'h': "[actu]",
'b': "[cgtu]",
'v': "[acg]",
'd': "[agtu]",
'n': "[acgtu]",
}
// DegenerateBaseMapNucl2 mappings nucleic acid degenerate base to all bases.
var DegenerateBaseMapNucl2 = map[byte]string{
'A': "A",
'T': "TU",
'U': "TU",
'C': "C",
'G': "G",
'R': "AG",
'Y': "CTU",
'M': "AC",
'K': "GTU",
'S': "CG",
'W': "ATU",
'H': "ACTU",
'B': "CGTU",
'V': "ACG",
'D': "AGTU",
'N': "ACGTU",
'a': "a",
't': "tu",
'u': "tu",
'c': "c",
'g': "g",
'r': "ag",
'y': "ctu",
'm': "ac",
'k': "gtu",
's': "cg",
'w': "atu",
'h': "actu",
'b': "cgtu",
'v': "acg",
'd': "agtu",
'n': "acgtu",
}
// DegenerateBaseMapProt mappings protein degenerate base to
// regular expression
var DegenerateBaseMapProt = map[byte]string{
'A': "A",
'B': "[DN]",
'C': "C",
'D': "D",
'E': "E",
'F': "F",
'G': "G",
'H': "H",
'I': "I",
'J': "[IL]",
'K': "K",
'L': "L",
'M': "M",
'N': "N",
'P': "P",
'Q': "Q",
'R': "R",
'S': "S",
'T': "T",
'V': "V",
'W': "W",
'X': "[A-Z]",
'Y': "Y",
'Z': "[QE]",
'a': "a",
'b': "[dn]",
'c': "c",
'd': "d",
'e': "e",
'f': "f",
'g': "g",
'h': "h",
'i': "i",
'j': "[il]",
'k': "k",
'l': "l",
'm': "m",
'n': "n",
'p': "p",
'q': "q",
'r': "r",
's': "s",
't': "t",
'v': "v",
'w': "w",
'x': "[a-z]",
'y': "y",
'z': "[qe]",
}
// Degenerate2Regexp transforms seqs containing degenrate base to regular expression
func (seq *Seq) Degenerate2Regexp() string {
var m map[byte]string
if seq.Alphabet == Protein {
m = DegenerateBaseMapProt
} else {
m = DegenerateBaseMapNucl
}
s := make([]string, len(seq.Seq))
for i, base := range seq.Seq {
if _, ok := m[base]; ok {
s[i] = m[base]
} else {
s[i] = string(base)
}
}
return strings.Join(s, "")
}
// Degenerate2Seqs transforms seqs containing degenrate bases to all possible sequences.
func Degenerate2Seqs(s []byte) (dseqs [][]byte, err error) {
dseqs = [][]byte{}
var i, j, k int
var ok bool
var dbases string
var dbase byte
for _, base := range s {
if dbases, ok = DegenerateBaseMapNucl2[base]; ok {
if len(dbases) == 1 {
dbase = dbases[0]
for i = 0; i < len(dseqs); i++ {
dseqs[i] = append(dseqs[i], dbase)
}
} else {
// 2nd
more := make([][]byte, len(dseqs)*(len(dbases)-1))
k = 0
for i = 1; i < len(dbases); i++ {
for j = 0; j < len(dseqs); j++ {
more[k] = []byte(string(append(dseqs[j], dbases[i])))
k++
}
}
// 1th
for i = 0; i < len(dseqs); i++ {
dseqs[i] = append(dseqs[i], dbases[0])
}
dseqs = append(dseqs, more...)
}
} else {
return dseqs, fmt.Errorf("seq: invalid letter: %c", base)
}
}
return dseqs, nil
}
// Translate translates the RNA/DNA to amino acid sequence.
// Available frame: 1, 2, 3, -1, -2 ,-3.
// If option trim is true, it removes all 'X' and '*' characters from the right end of the translation.
// If option clean is true, it changes all STOP codon positions from the '*' character to 'X' (an unknown residue).
// If option allowUnknownCodon is true, codons not in the codon table will be translated to 'X'.
// If option markInitCodonAsM is true, initial codon at beginning will be represented as 'M'.
func (seq *Seq) Translate(transl_table int, frame int, trim bool, clean bool, allowUnknownCodon bool, markInitCodonAsM bool) (*Seq, error) {
if !(seq.Alphabet.String() == "DNA" || seq.Alphabet.String() == "DNAredundant" || seq.Alphabet.String() == "RNA" || seq.Alphabet.String() == "RNAredundant") {
return nil, fmt.Errorf("seq: only DNA/RNA sequence can all method Translate, the alphabet is %s", seq.Alphabet.String())
}
var codonTable *CodonTable
var ok bool
if codonTable, ok = CodonTables[transl_table]; !ok {
return nil, fmt.Errorf("seq: invalid codon table: %d", transl_table)
}
if !(frame == 1 || frame == 2 || frame == 3 || frame == -1 || frame == -2 || frame == -3) {
return nil, fmt.Errorf("seq: invalid frame: %d. available: 1, 2, 3, -1, -2, -3", frame)
}
aa, err := codonTable.Translate(seq.Seq, frame, trim, clean, allowUnknownCodon, markInitCodonAsM)
if err != nil {
return nil, err
}
t, err := NewSeqWithoutValidation(Protein, aa)
if err != nil {
return nil, err
}
return t, nil
}
// ParseQual parses sequence quality, asciiBase = 33 for Phred+33.
func (seq *Seq) ParseQual(asciiBase int) {
if len(seq.Qual) == 0 {
return
}
if seq.QualValue != nil {
seq.QualValue = seq.QualValue[:0]
for _, q := range seq.Qual {
seq.QualValue = append(seq.QualValue, int(q)-asciiBase)
}
return
}
qv := make([]int, len(seq.Qual))
for i, q := range seq.Qual {
qv[i] = int(q) - asciiBase
}
seq.QualValue = qv
}
// AvgQual calculates average quality value.
func (seq *Seq) AvgQual(asciiBase int) float64 {
if len(seq.Qual) > 0 {
seq.ParseQual(asciiBase)
}
if len(seq.QualValue) == 0 {
return 0.0
}
var sum float64
for _, q := range seq.QualValue {
sum += QUAL_MAP[q]
}
return -10 * math.Log10(sum/float64(len(seq.QualValue)))
}
// Slider returns a function for sliding the sequence.
// Circular is for circular genome, and it overides greedy.
// If not circular and greedy is true, last fragment shorter than window will be returned.
func (seq *Seq) Slider(window int, step int, circular bool, greedy bool) func() (*Seq, bool) {
alphabet := seq.Alphabet
originalLen := len(seq.Seq)
sequence := seq.Seq
qual := seq.Qual
fastq := len(qual) > 0
l := len(sequence)
end := l - 1
if end < 0 {
end = 0
}
var i, e int
var s, q []byte
i = 0
return func() (*Seq, bool) {
if i > end {
return nil, false
}
e = i + window
if e > originalLen {
if circular {
e = e - originalLen
s = sequence[i:]
s = append(s, sequence[0:e]...)
if fastq {
q = qual[i:]
q = append(q, qual[0:e]...)
}
} else if greedy {
s = sequence[i:]
if fastq {
q = qual[i:]
}
e = l
} else { // end
return nil, false
}
} else {
s = sequence[i : i+window]
if fastq {
q = qual[i : i+window]
}
}
i += step
var newseq *Seq
if fastq {
newseq, _ = NewSeqWithQualWithoutValidation(alphabet, s, q)
return newseq, true
}
newseq, _ = NewSeqWithoutValidation(alphabet, s)
return newseq, true
}
}
bio-0.13.3/seq/seq_test.go 0000775 0000000 0000000 00000006607 14573550650 0015343 0 ustar 00root root 0000000 0000000 package seq
import (
"fmt"
"testing"
)
func TestValidateSequence(t *testing.T) {
dna := []byte("acgt")
dna2 := []byte("ACGTRYMKSWHBVDN")
rna := []byte("acgu")
fake := []byte("acgturymkswhbvdnz")
ok := DNA.IsValid(dna) == nil &&
DNAredundant.IsValid(dna2) == nil &&
RNA.IsValid(rna) == nil &&
RNA.IsValid(fake) != nil
if !ok {
t.Error("validate sequence failed.")
return
}
}
func TestRevCom(t *testing.T) {
dna, _ := NewSeq(DNA, []byte("acgtccn-"))
if string(dna.RevCom().Seq) != "-nggacgt" {
t.Error("revcom sequence failed.")
return
}
rna, _ := NewSeq(RNA, []byte("auguccn-"))
if string(rna.RevCom().Seq) != "-nggacau" {
t.Error("revcom sequence failed.")
return
}
}
func TestBaseContent(t *testing.T) {
dna, _ := NewSeq(DNA, []byte("acgtACGT"))
content := dna.BaseContent("gc")
wanted := 0.5
if content != wanted {
t.Error(fmt.Printf("compution of base content failed: %f != %f", content, wanted))
return
}
}
func TestSubSeq(t *testing.T) {
s, _ := NewSeqWithoutValidation(DNA, []byte("ACGTNacgtn"))
ok := string(s.SubSeq(1, 1).Seq) == "A" &&
string(s.SubSeq(2, 4).Seq) == "CGT" &&
string(s.SubSeq(-4, -2).Seq) == "cgt" &&
string(s.SubSeq(-4, -1).Seq) == "cgtn" &&
string(s.SubSeq(-1, -1).Seq) == "n" &&
string(s.SubSeq(2, -2).Seq) == "CGTNacgt" &&
string(s.SubSeq(1, -1).Seq) == "ACGTNacgtn" &&
string(s.SubSeq(12, 14).Seq) == "" &&
string(s.SubSeq(-10, -1).Seq) == "ACGTNacgtn" &&
string(s.SubSeq(-10, -3).Seq) == "ACGTNacg" &&
string(s.SubSeq(1, 10).Seq) == "ACGTNacgtn" &&
string(s.SubSeq(3, 12).Seq) == "GTNacgtn" &&
string(s.SubSeq(3, 100).Seq) == "GTNacgtn"
if !ok {
t.Error(fmt.Printf("subseq error"))
}
ok = string(s.SubSeq(-4, 2).Seq) == "" &&
string(s.SubSeq(-3, -4).Seq) == ""
if !ok {
t.Error(fmt.Printf("subseq error"))
}
s, _ = NewSeqWithoutValidation(DNA, []byte(""))
ok = string(s.SubSeq(1, 4).Seq) == "" &&
string(s.SubSeq(2, 4).Seq) == "" &&
string(s.SubSeq(1, -1).Seq) == "" &&
string(s.SubSeq(-4, -1).Seq) == ""
if !ok {
t.Error(fmt.Printf("subseq error"))
}
}
func TestSubSeqInplace(t *testing.T) {
s, _ := NewSeqWithoutValidation(DNA, []byte("ACGTNacgtn"))
ok := string(s.Clone().SubSeqInplace(1, 1).Seq) == "A" &&
string(s.Clone().SubSeqInplace(2, 4).Seq) == "CGT" &&
string(s.Clone().SubSeqInplace(-4, -2).Seq) == "cgt" &&
string(s.Clone().SubSeqInplace(-4, -1).Seq) == "cgtn" &&
string(s.Clone().SubSeqInplace(-1, -1).Seq) == "n" &&
string(s.Clone().SubSeqInplace(2, -2).Seq) == "CGTNacgt" &&
string(s.Clone().SubSeqInplace(1, -1).Seq) == "ACGTNacgtn" &&
string(s.Clone().SubSeqInplace(-10, -1).Seq) == "ACGTNacgtn" &&
string(s.Clone().SubSeqInplace(-10, -3).Seq) == "ACGTNacg" &&
string(s.Clone().SubSeqInplace(1, 10).Seq) == "ACGTNacgtn" &&
string(s.Clone().SubSeqInplace(3, 10).Seq) == "GTNacgtn" &&
string(s.Clone().SubSeqInplace(3, 100).Seq) == "GTNacgtn"
if !ok {
t.Error(fmt.Printf("SubSeqInplace error"))
}
ok = string(s.Clone().SubSeqInplace(-4, 2).Seq) == "" &&
string(s.Clone().SubSeqInplace(-3, -4).Seq) == ""
if !ok {
t.Error(fmt.Printf("SubSeqInplace error"))
}
s, _ = NewSeqWithoutValidation(DNA, []byte(""))
ok = string(s.Clone().SubSeqInplace(1, 4).Seq) == "" &&
string(s.Clone().SubSeqInplace(2, 4).Seq) == "" &&
string(s.Clone().SubSeqInplace(1, -1).Seq) == "" &&
string(s.Clone().SubSeqInplace(-4, -1).Seq) == ""
if !ok {
t.Error(fmt.Printf("subseq error"))
}
}
bio-0.13.3/seqio/ 0000775 0000000 0000000 00000000000 14573550650 0013501 5 ustar 00root root 0000000 0000000 bio-0.13.3/seqio/fai/ 0000775 0000000 0000000 00000000000 14573550650 0014240 5 ustar 00root root 0000000 0000000 bio-0.13.3/seqio/fai/README.md 0000775 0000000 0000000 00000006654 14573550650 0015535 0 ustar 00root root 0000000 0000000 # fai
[](https://godoc.org/github.com/shenwei356/bio/seqio/fai)
Package fai implements fasta sequence file index handling, including creating
, reading and random accessing.
Code of fai data structure were copied and edited from [1].
But I wrote the code of creating and reading fai, and so did test code.
Code of random accessing subsequences were copied from [2], but I extended them a lot.
Reference:
[1]. https://github.com/biogo/biogo/blob/master/io/seqio/fai/fai.go
[2]. https://github.com/brentp/faidx/blob/master/faidx.go
## General Usage
import "github.com/shenwei356/bio/seqio/fai"
file := "seq.fa"
faidx, err := fai.New(file)
checkErr(err)
defer func() {
checkErr(faidx.Close())
}()
// whole sequence
seq, err := faidx.Seq("cel-mir-2")
checkErr(err)
// single base
s, err := faidx.Base("cel-let-7", 1)
checkErr(err)
// subsequence. start and end are all 1-based
seq, err := faidx.SubSeq("cel-mir-2", 15, 19)
checkErr(err)
## Extended SubSeq
For extended SubSeq, negative position is allowed.
This is my custom locating strategy. Start and end are all 1-based.
To better understand the locating strategy, see examples below:
1-based index 1 2 3 4 5 6 7 8 9 10
negative index 0-9-8-7-6-5-4-3-2-1
seq A C G T N a c g t n
1:1 A
2:4 C G T
-4:-2 c g t
-4:-1 c g t n
-1:-1 n
2:-2 C G T N a c g t
1:-1 A C G T N a c g t n
Examples:
// last 12 bases
seq, err := faidx.SubSeq("cel-mir-2", -12, -1)
checkErr(err)
## Advanced Usage
Function `fai.New(file string)` is a wraper to simplify the process of
creating and reading FASTA index . Let's see what's happend inside:
func New(file string) (*Faidx, error) {
fileFai := file + ".fai"
var index Index
if _, err := os.Stat(fileFai); os.IsNotExist(err) {
index, err = Create(file)
if err != nil {
return nil, err
}
} else {
index, err = Read(fileFai)
if err != nil {
return nil, err
}
}
return NewWithIndex(file, index)
}
By default, sequence ID is used as key in FASTA index file.
Inside the package, a regular expression is used to get sequence ID from
full head. The default value is `^([^\s]+)\s?`, i.e. getting
first non-space characters of head.
So you can just use `fai.Create(file string)` to create .fai file.
If you want to use full head instead of sequence ID (first non-space characters of head),
you could use `fai.CreateWithIDRegexp(file string, idRegexp string)` to create faidx.
Here, the `idRegexp` should be `^(.+)$`. For convenience, you can use another function
`CreateWithFullHead`.
## More Advanced Usages
Note that, ***by default, whole file is mapped into shared memory***,
which is OK for small files (smaller than your RAM).
For very big files, you should disable that.
Instead, file seeking is used.
// change the global variable
fai.MapWholeFile = false
// then do other things
## Documentation
[Documentation on godoc](https://godoc.org/github.com/shenwei356/bio/seqio/fai).
bio-0.13.3/seqio/fai/doc.go 0000664 0000000 0000000 00000006453 14573550650 0015344 0 ustar 00root root 0000000 0000000 /*Package fai implements fasta sequence file index handling, including creating
, reading and random accessing.
Code of fai data structure were copied and edited from [1].
But I wrote the code of creating and reading fai, and so did test code.
Code of random accessing subsequences were copied from [2], but I extended them a lot.
Reference:
[1]. https://github.com/biogo/biogo/blob/master/io/seqio/fai/fai.go
[2]. https://github.com/brentp/faidx/blob/master/faidx.go
## General Usage
import "github.com/shenwei356/bio/seqio/fai"
file := "seq.fa"
faidx, err := fai.New(file)
checkErr(err)
defer func() {
checkErr(faidx.Close())
}()
// whole sequence
seq, err := faidx.Seq("cel-mir-2")
checkErr(err)
// single base
s, err := faidx.Base("cel-let-7", 1)
checkErr(err)
// subsequence. start and end are all 1-based
seq, err := faidx.SubSeq("cel-mir-2", 15, 19)
checkErr(err)
## Extended SubSeq
For extended SubSeq, negative position is allowed.
This is my custom locating strategy. Start and end are all 1-based.
To better understand the locating strategy, see examples below:
1-based index 1 2 3 4 5 6 7 8 9 10
negative index 0-9-8-7-6-5-4-3-2-1
seq A C G T N a c g t n
1:1 A
2:4 C G T
-4:-2 c g t
-4:-1 c g t n
-1:-1 n
2:-2 C G T N a c g t
1:-1 A C G T N a c g t n
1:12 A C G T N a c g t n
-12:-1 A C G T N a c g t n
Examples:
// last 12 bases
seq, err := faidx.SubSeq("cel-mir-2", -12, -1)
checkErr(err)
## Advanced Usage
Function `fai.New(file string)` is a wraper to simplify the process of
creating and reading FASTA index . Let's see what's happened inside:
func New(file string) (*Faidx, error) {
fileFai := file + ".fai"
var index Index
if _, err := os.Stat(fileFai); os.IsNotExist(err) {
index, err = Create(file)
if err != nil {
return nil, err
}
} else {
index, err = Read(fileFai)
if err != nil {
return nil, err
}
}
return NewWithIndex(file, index)
}
By default, sequence ID is used as key in FASTA index file.
Inside the package, a regular expression is used to get sequence ID from
full head. The default value is `^([^\s]+)\s?`, i.e. getting
first non-space characters of head.
So you can just use `fai.Create(file string)` to create .fai file.
If you want to use full head instead of sequence ID (first non-space characters of head),
you could use `fai.CreateWithIDRegexp(file string, idRegexp string)` to create faidx.
Here, the `idRegexp` should be `^(.+)$`. For convenience, you can use another function
`CreateWithFullHead`.
## More Advanced Usages
Note that, ***by default, whole file is mapped into shared memory***,
which is OK for small files (smaller than your RAM).
For very big files, you should disable that.
Instead, file seeking is used.
// change the global variable
fai.MapWholeFile = false
// then do other things
*/
package fai
bio-0.13.3/seqio/fai/fai.go 0000775 0000000 0000000 00000020164 14573550650 0015334 0 ustar 00root root 0000000 0000000 package fai
import (
"bufio"
"bytes"
"fmt"
"os"
"regexp"
"strconv"
"strings"
)
// Record is FASTA index record
type Record struct {
Name string
Length int
Start int64
BasesPerLine int
BytesPerLine int
}
// Index is FASTA index
type Index map[string]Record
// Read faidx from .fai file
func Read(fileFai string) (Index, error) {
fh, err := os.Open(fileFai)
if err != nil {
return nil, fmt.Errorf("read faidx: %s", err)
}
defer fh.Close()
index := make(map[string]Record)
scanner := bufio.NewScanner(fh)
items := make([]string, 5)
var line, name string
var length int
var start int64
var BasesPerLine, bytesPerLine int
for scanner.Scan() {
line = scanner.Text()
if line != "" {
line = dropCRStr(line)
stringSplitNByByte(line, '\t', 5, &items)
if len(items) != 5 {
return nil, fmt.Errorf("invalid fai records: %s", line)
}
name = items[0]
length, err = strconv.Atoi(items[1])
if err != nil {
return nil, fmt.Errorf("invalid fai records: %s", line)
}
start, err = strconv.ParseInt(items[2], 10, 64)
if err != nil {
return nil, fmt.Errorf("invalid fai records: %s", line)
}
BasesPerLine, err = strconv.Atoi(items[3])
if err != nil {
return nil, fmt.Errorf("invalid fai records: %s", line)
}
bytesPerLine, err = strconv.Atoi(items[4])
if err != nil {
return nil, fmt.Errorf("invalid fai records: %s", line)
}
index[name] = Record{
Name: name,
Length: length,
Start: start,
BasesPerLine: BasesPerLine,
BytesPerLine: bytesPerLine,
}
}
if err := scanner.Err(); err != nil {
return nil, err
}
}
return index, nil
}
// CreateWithFullHead uses full head instead of just sequence ID
func CreateWithFullHead(fileSeq, fileFai string) (Index, error) {
return CreateWithIDRegexp(fileSeq, fileFai, `^(.+)$`)
}
// CreateWithIDRegexp uses custom regular expression to get sequence ID
func CreateWithIDRegexp(fileSeq, fileFai string, idRegexp string) (Index, error) {
if idRegexp != defaultIDRegexp {
if !reCheckIDregexpStr.MatchString(idRegexp) {
return nil, fmt.Errorf(`regular expression must contain "(" and ")" to capture matched ID. default: %s`, `^([^\s]+)\s?`)
}
var err error
IDRegexp, err = regexp.Compile(idRegexp)
if err != nil {
return nil, fmt.Errorf("fail to Compile idRegexp: %s", err)
}
isUsingDefaultIDRegexp = false
}
return Create(fileSeq, fileFai)
}
// Create .fai for file
func Create(fileSeq, fileFai string) (Index, error) {
fh, err := os.Open(fileSeq)
if err != nil {
return nil, fmt.Errorf("fail to open seq file: %s", err)
}
defer fh.Close()
outfh, err := os.Create(fileFai)
if err != nil {
return nil, fmt.Errorf("fail to write fai file: %s", err)
}
defer outfh.Close()
index := make(map[string]Record)
reader := bufio.NewReader(fh)
checkSeqType := true
seqLen := 0
var hasSeq bool
var lastName, thisName []byte
var id string
var lastStart, thisStart int64
var lineWidths, seqWidths []int
var lastLineWidth, lineWidth, seqWidth int
var chances int
var line, lineDropCR []byte
var seenSeqs bool
for {
line, err = reader.ReadBytes('\n')
if err != nil { // end of file
id = string(parseHeadID(lastName))
if strings.Contains(id, "\t") {
id = reTabs.ReplaceAllString(id, " ")
}
// check lineWidths
lastLineWidth, chances = -2, 2
seenSeqs = false
for i := len(lineWidths) - 1; i >= 0; i-- {
if !seenSeqs && seqWidths[i] == 0 { // skip empty lines in the end
continue
}
seenSeqs = true
if lastLineWidth == -2 {
lastLineWidth = lineWidths[i]
continue
}
if lineWidths[i] != lastLineWidth {
chances--
if chances == 0 || lineWidths[i] < lastLineWidth {
return nil, fmt.Errorf("different line length in sequence: %s. Please format the file with 'seqkit seq'", id)
}
}
lastLineWidth = lineWidths[i]
}
// lineWidth = 0
if len(lineWidths) > 0 {
lineWidth = lineWidths[0]
}
// seqWidth = 0
if len(seqWidths) > 0 {
seqWidth = seqWidths[0]
}
if len(line) > 0 && line[len(line)-1] != '\n' {
fmt.Fprintln(os.Stderr, `[WARNING]: newline character ('\n') not detected at end of file, truncated file?`)
}
seqLen += len(line)
if _, ok := index[id]; ok {
// return index, fmt.Errorf(`ignoring duplicate sequence "%s" at byte offset %d`, id, lastStart)
os.Stderr.WriteString(fmt.Sprintf("[fai warning] ignoring duplicate sequence \"%s\" at byte offset %d\n", id, lastStart))
} else {
fmt.Fprintf(outfh, "%s\t%d\t%d\t%d\t%d\n", id, seqLen, lastStart, seqWidth, lineWidth)
index[id] = Record{
Name: id,
Length: seqLen,
Start: lastStart,
BasesPerLine: seqWidth,
BytesPerLine: lineWidth,
}
}
seqLen = 0
break
}
if checkSeqType {
if line[0] == '@' {
os.Remove(fileFai)
return nil, fmt.Errorf("FASTQ format not supported")
}
checkSeqType = false
}
if line[0] == '>' {
hasSeq = true
thisName = dropCR(line[1 : len(line)-1])
if lastName != nil { // not the first record
id = string(parseHeadID(lastName))
if strings.Contains(id, "\t") {
id = reTabs.ReplaceAllString(id, " ")
}
// check lineWidths
lastLineWidth, chances = -1, 2
seenSeqs = false
for i := len(lineWidths) - 1; i >= 0; i-- {
if !seenSeqs && seqWidths[i] == 0 { // skip empty lines in the end
continue
}
seenSeqs = true
if lastLineWidth == -1 {
lastLineWidth = lineWidths[i]
continue
}
if lineWidths[i] != lastLineWidth {
chances--
if chances == 0 || lineWidths[i] < lastLineWidth {
return nil, fmt.Errorf("different line length in sequence: %s. Please format the file with 'seqkit seq'", id)
}
}
lastLineWidth = lineWidths[i]
}
// lineWidth = 0
if len(lineWidths) > 0 {
lineWidth = lineWidths[0]
}
// seqWidth = 0
if len(seqWidths) > 0 {
seqWidth = seqWidths[0]
}
if _, ok := index[id]; ok {
// return index, fmt.Errorf(`ignoring duplicate sequence "%s" at byte offset %d`, id, lastStart)
os.Stderr.WriteString(fmt.Sprintf("[fai warning] ignoring duplicate sequence \"%s\" at byte offset %d\n", id, lastStart))
} else {
fmt.Fprintf(outfh, "%s\t%d\t%d\t%d\t%d\n", id, seqLen, lastStart, seqWidth, lineWidth)
index[id] = Record{
Name: id,
Length: seqLen,
Start: lastStart,
BasesPerLine: seqWidth,
BytesPerLine: lineWidth,
}
}
seqLen = 0
}
lineWidths = []int{}
seqWidths = []int{}
thisStart += int64(len(line))
lastStart = thisStart
lastName = thisName
} else if hasSeq {
lineDropCR = dropCR(line[0 : len(line)-1])
seqLen += len(lineDropCR)
thisStart += int64(len(line))
lineWidths = append(lineWidths, len(line))
seqWidths = append(seqWidths, len(lineDropCR))
} else {
return nil, fmt.Errorf("invalid fasta file: %s", fileSeq)
}
}
return index, nil
}
// ------------------------------------------------------------
var reCheckIDregexpStr = regexp.MustCompile(`\(.+\)`)
var defaultIDRegexp = `^(\S+)\s?`
var reTabs = regexp.MustCompile(`\t+`)
// IDRegexp is regexp for parsing record id
var IDRegexp = regexp.MustCompile(defaultIDRegexp)
var isUsingDefaultIDRegexp = true
func parseHeadID(head []byte) []byte {
if isUsingDefaultIDRegexp {
if i := bytes.IndexByte(head, ' '); i > 0 {
return head[0:i]
}
if i := bytes.IndexByte(head, '\t'); i > 0 {
return head[0:i]
}
return head
}
found := IDRegexp.FindSubmatch(head)
if found == nil { // not match
return head
}
return found[1]
}
func dropCR(data []byte) []byte {
if len(data) > 0 && data[len(data)-1] == '\r' {
return data[0 : len(data)-1]
}
return data
}
func dropCRStr(data string) string {
if len(data) > 0 && data[len(data)-1] == '\r' {
return data[0 : len(data)-1]
}
return data
}
func stringSplitNByByte(s string, sep byte, n int, a *[]string) {
if a == nil {
tmp := make([]string, n)
a = &tmp
}
n--
i := 0
for i < n {
m := strings.IndexByte(s, sep)
if m < 0 {
break
}
(*a)[i] = s[:m]
s = s[m+1:]
i++
}
(*a)[i] = s
(*a) = (*a)[:i+1]
}
bio-0.13.3/seqio/fai/faidx.go 0000775 0000000 0000000 00000011462 14573550650 0015671 0 ustar 00root root 0000000 0000000 package fai
import (
"fmt"
"io"
"os"
"github.com/edsrzf/mmap-go"
)
// MapWholeFile is a globle flag to decides whether map whole file
var MapWholeFile = true
var pageSize = int64(os.Getpagesize())
var pageSizeInt = os.Getpagesize()
// Faidx is
type Faidx struct {
file string
reader *os.File
Index Index
mmap mmap.MMap
}
// New try to get Faidx from fasta file
func New(fileSeq string) (*Faidx, error) {
fileFai := fileSeq + ".fai"
return NewWithCustomExt(fileSeq, fileFai)
}
// NewWithCustomExt try to get Faidx from fasta file, and .fai is specified
func NewWithCustomExt(fileSeq, fileFai string) (*Faidx, error) {
var index Index
if _, err := os.Stat(fileFai); os.IsNotExist(err) {
index, err = Create(fileSeq, fileFai)
if err != nil {
return nil, err
}
} else {
index, err = Read(fileFai)
if err != nil {
return nil, err
}
}
return NewWithIndex(fileSeq, index)
}
// NewWithIndex return faidx from file and readed Index.
// Useful for using custom IDRegexp
func NewWithIndex(file string, index Index) (*Faidx, error) {
reader, err := os.Open(file)
if err != nil {
return nil, fmt.Errorf("fail to open seq file: %s", err)
}
var m mmap.MMap
if MapWholeFile {
m, err = mmap.Map(reader, mmap.RDONLY, 0)
if err != nil {
return nil, fmt.Errorf("mmap err: %s", err)
}
}
return &Faidx{file, reader, index, m}, nil
}
// p is 0-based
func position(r Record, p int) int64 {
if p < 0 {
p = 0
}
if p > r.Length {
p = r.Length
}
return r.Start + int64(p/r.BasesPerLine*r.BytesPerLine+p%r.BasesPerLine)
}
// ErrSeqNotExists means that sequence not exists
var ErrSeqNotExists = fmt.Errorf("sequence not exists")
// SubSeq returns subsequence of chr from start to end. start and end are 1-based.
func (f *Faidx) SubSeq(chr string, start int, end int) ([]byte, error) {
sequence, err := f.SubSeqNotCleaned(chr, start, end)
if err != nil {
return nil, err
}
return cleanSeq(sequence), nil
}
// SubSeqNotCleaned returns subsequence of chr from start to end.
// start and end are 1-based.
// "\r" and "\n" are not cleaned.
func (f *Faidx) SubSeqNotCleaned(chr string, start int, end int) ([]byte, error) {
index, ok := f.Index[chr]
if !ok {
return nil, ErrSeqNotExists
}
if index.Length == 0 {
return []byte{}, nil
}
start, end, ok = SubLocation(index.Length, start, end)
if !ok {
return []byte{}, nil
}
pstart := position(index, start-1)
pend := position(index, end)
if MapWholeFile {
if pend > int64(len(f.mmap)) { // for truncated file
pend = int64(len(f.mmap))
}
return f.mmap[pstart:pend], nil
}
data := make([]byte, pend-pstart)
n, err := f.reader.ReadAt(data, pstart)
if err != nil {
if err == io.EOF { // for truncated file
return data[0:n], nil
}
return nil, err
}
return data, nil
}
// Seq returns sequence of chr
func (f *Faidx) Seq(chr string) ([]byte, error) {
sequence, err := f.SeqNotCleaned(chr)
if err != nil {
return nil, err
}
return cleanSeq(sequence), nil
}
// SeqNotCleaned returns sequences without cleaning "\r", and "\n"
func (f *Faidx) SeqNotCleaned(chr string) ([]byte, error) {
sequence, err := f.SubSeqNotCleaned(chr, 1, -1)
if err != nil {
return nil, err
}
return sequence, nil
}
// Base returns base in position pos. pos is 1 based
func (f *Faidx) Base(chr string, pos int) (byte, error) {
sequence, err := f.SubSeqNotCleaned(chr, pos, pos)
if err != nil {
return ' ', err
}
return sequence[0], nil
}
// Close the readers
func (f *Faidx) Close() error {
f.reader.Close()
if f.mmap == nil {
return nil
}
return f.mmap.Unmap()
}
/*SubLocation is my sublocation strategy,
start, end and returned start and end are all 1-based
1-based index 1 2 3 4 5 6 7 8 9 10
negative index 0-9-8-7-6-5-4-3-2-1
seq A C G T N a c g t n
1:1 A
2:4 C G T
-4:-2 c g t
-4:-1 c g t n
-1:-1 n
2:-2 C G T N a c g t
1:-1 A C G T N a c g t n
1:12 A C G T N a c g t n
-12:-1 A C G T N a c g t n
*/
func SubLocation(length, start, end int) (int, int, bool) {
if length == 0 {
return 0, 0, false
}
if start < 1 {
if start == 0 {
start = 1
} else if start < 0 {
if end < 0 && start > end {
return start, end, false
}
if -start > length {
return start, end, false
}
start = length + start + 1
}
}
if start > length {
return start, end, false
}
if end > length {
end = length
}
if end < 1 {
if end == 0 {
end = -1
}
end = length + end + 1
}
if start-1 > end {
return start - 1, end, false
}
return start, end, true
}
func cleanSeq(slice []byte) []byte {
newSlice := make([]byte, 0, len(slice))
for _, b := range slice {
switch b {
case '\r', '\n':
default:
newSlice = append(newSlice, b)
}
}
return newSlice
}
bio-0.13.3/seqio/fai/faidx_test.go 0000775 0000000 0000000 00000006407 14573550650 0016733 0 ustar 00root root 0000000 0000000 package fai
import (
"bytes"
"testing"
"github.com/shenwei356/bio/seqio/fastx"
)
func TestFastaReader(t *testing.T) {
file := "seq.fa"
idx, err := New(file)
if err != nil {
t.Errorf("failed to create faidx for %s: %s", file, err)
return
}
// all sequences
seqs, err := fastx.GetSeqs(file, nil, 4, 10, fastx.DefaultIDRegexp)
if err != nil {
t.Errorf("failed to read seqs: %v", err)
}
for _, rec := range seqs {
seq, err := idx.Seq(string(rec.ID))
checkErr(t, err)
if !bytes.Equal(seq, rec.Seq.Seq) {
t.Errorf("unmatched sequences %s: %s", rec.ID, seq)
}
}
//
chr := "cel-let-7"
s, err := idx.Base(chr, 1)
checkErr(t, err)
if s != 'U' {
t.Errorf("unmatched sequences %s: %s", chr, []byte{s})
}
chr = "blank"
seq, err := idx.Seq(chr)
checkErr(t, err)
if string(seq) != "" {
t.Errorf("unmatched sequences %s: %s", chr, seq)
}
chr = "cel-mir-2"
seq, err = idx.Seq(chr)
checkErr(t, err)
if string(seq) != "UAAACAGUAUACAGAAAGCCAUCAAAGC" {
t.Errorf("unmatched sequences %s: %s", chr, seq)
}
start, end := 15, 19
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "AAAGC" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = -3, -1
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "AGC" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = 1, -1
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "UAAACAGUAUACAGAAAGCCAUCAAAGC" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = 2, -2
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "AAACAGUAUACAGAAAGCCAUCAAAG" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = 20, -2
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "CAUCAAAG" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = 50, -2
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
chr = "seq"
seq, err = idx.Seq(chr)
checkErr(t, err)
if string(seq) != "ACTGACTG" {
t.Errorf("unmatched sequences %s: %s", chr, seq)
}
err = idx.Close()
if err != nil {
t.Errorf("fail to close faidx: %v", err)
}
}
func TestFastaReaderNotMapWholeFile(t *testing.T) {
MapWholeFile = false
TestFastaReader(t)
MapWholeFile = true
}
func TestFastaReader2NotMapWholeFile(t *testing.T) {
MapWholeFile = false
TestFastaReader2(t)
MapWholeFile = true
}
func checkErr(t *testing.T, err error) {
if err != nil {
t.Error(err)
}
}
func TestFastaReader2(t *testing.T) {
file := "seq2.fa"
idx, err := New(file)
if err != nil {
t.Errorf("failed to create faidx for %s: %s", file, err)
return
}
seqs, err := fastx.GetSeqs(file, nil, 4, 10, fastx.DefaultIDRegexp)
if err != nil {
t.Errorf("failed to read seqs: %v", err)
}
for _, rec := range seqs {
seq, err := idx.Seq(string(rec.ID))
checkErr(t, err)
if !bytes.Equal(seq, rec.Seq.Seq) {
t.Errorf("unmatched sequences %s: %s", rec.ID, seq)
}
}
err = idx.Close()
if err != nil {
t.Errorf("fail to close faidx: %v", err)
}
}
bio-0.13.3/seqio/fai/seq.fa 0000664 0000000 0000000 00000001403 14573550650 0015336 0 ustar 00root root 0000000 0000000 >cel-let-7 MI0000001 Caenorhabditis elegans let-7 stem-loop
UACACUGUGGAUCCGGUGAGGUAGUAGGUUCC
GUAUAGUUUGGAAUAUUACCACCGGUGAACCC
UAUGCAAUUUUCUACCUUACCGGAGACAGACC
ACUCUUCGA
>cel-lin-4 MI0000002 Caenorhabditis elegans lin-4 stem-loop
AUGCUUCCGGCCUGUUCCCUGAGACCUCAA
GUGUGAGUGUACUAUUGAUGCUUCACACCU
GGGCUCUCCGGGUACCAGGACGGUUUGAGC
AGAU
>blank
>cel-mir-1 MI0000003 Caenorhabditis elegans miR-1 stem-loop
AAAGUGACCGUACCGAGCUGCAUACUUCCUAAA
UACAUGCCCAUACUAUAUCAUAAAUGGAUAAAA
UGGAAUGUAAAGAAGUAUGUAGAACGGGGUAAA
GGUAGU
>cel-mir-2 MI0000004 Caenorhabditis elegans miR-2 stem-loop
UAAACAGUAUAC
AGAAAGCCAUCA
AAGC
>cel-mir-34 MI0000005 Caenorhabditis elegans miR-34 stem-loop
CGGACAAUGCUCGAGAGGCAGUGUGGUUAG
CUGGUUGCAUAUUUCCUUGACAACGGCUAC
CUUCACUGCCACCCCGAACAUGUCGUCCAU
CUUUGAA
>seq
ACTG
ACTG bio-0.13.3/seqio/fai/seq.fa.fai 0000664 0000000 0000000 00000000225 14573550650 0016075 0 ustar 00root root 0000000 0000000 cel-let-7 105 60 32 33
cel-lin-4 94 229 30 31
blank 0 334 30 31
cel-mir-1 105 394 33 34
cel-mir-2 28 563 12 13
cel-mir-34 97 656 30 31
seq 8 762 4 5
bio-0.13.3/seqio/fai/seq2.fa 0000664 0000000 0000000 00000000061 14573550650 0015417 0 ustar 00root root 0000000 0000000 >s1
acgt
ACGT
ac
>s2
>s3
>s4
acccc
accc
>s5
a
bio-0.13.3/seqio/fai/seq2.fa.fai 0000664 0000000 0000000 00000000074 14573550650 0016161 0 ustar 00root root 0000000 0000000 s1 10 4 4 5
s2 0 22 0 1
s3 0 27 0 1
s4 9 31 5 6
s5 1 47 1 2
bio-0.13.3/seqio/fastx/ 0000775 0000000 0000000 00000000000 14573550650 0014626 5 ustar 00root root 0000000 0000000 bio-0.13.3/seqio/fastx/README.md 0000775 0000000 0000000 00000004420 14573550650 0016110 0 ustar 00root root 0000000 0000000 # fastx
[](https://pkg.go.dev/github.com/shenwei356/bio/seqio/fastx)
This package seamlessly parses both FASTA and FASTQ formats.
## Examples
### Common operation
package main
import (
"fmt"
"io"
"os"
// "github.com/shenwei356/bio/seq"
"github.com/shenwei356/bio/seqio/fastx"
"github.com/shenwei356/xopen"
)
func main() {
// use buffered out stream for output
outfh, err := xopen.Wopen("-") // "-" for STDOUT
checkError(err)
defer outfh.Close()
// disable sequence validation could reduce time when reading large sequences
// seq.ValidateSeq = false
reader, err := fastx.NewDefaultReader("-")
checkError(err)
var record *fastx.Record
for {
record, err = reader.Read()
if err != nil {
if err == io.EOF {
break
}
checkError(err)
break
}
// fmt is slow for output, because it's not buffered
// fmt.Printf("%s", record.Format(0))
record.FormatToWriter(outfh, 0)
}
reader.Close() // Please remember to call this !!!
}
func checkError(err error) {
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
}
***Note that***, similar with `bytes.Buffer.Bytes()` method,
the current record will change after your another call of this method.
You may use `record.Clone()` to make a copy.
### Asynchronously parsing
`ChunkChan` asynchronously reads FASTA/Q records, and returns a channel of
Record Chunk, from which you can easily access the records.
`bufferSize` is the number of buffered chunks, and `chunkSize` is the size
of records in a chunk.
reader, err := fastx.NewDefaultReader(file)
checkError(err)
for chunk := range reader.ChunkChan(bufferSize, chunkSize) {
checkError(chunk.Err)
for _, record := range chunk.Data {
fmt.Print(record)
}
}
***Note that***, these's no need to clone the record by `record.Clone()` here.
### Custom alphabet and identifier regular expression
import (
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/bio/seqio/fastx"
)
reader, err := fastx.NewReader(seq.DNA, file, "^([^\s]+)\s?")
bio-0.13.3/seqio/fastx/blank.fx 0000664 0000000 0000000 00000000002 14573550650 0016244 0 ustar 00root root 0000000 0000000
bio-0.13.3/seqio/fastx/blank1.fx 0000664 0000000 0000000 00000000001 14573550650 0016324 0 ustar 00root root 0000000 0000000
bio-0.13.3/seqio/fastx/doc.go 0000664 0000000 0000000 00000004166 14573550650 0015731 0 ustar 00root root 0000000 0000000 /*Package fastx seamlessly parses FASTA and FASTQ format file
This package seamlessly parses both FASTA and FASTQ formats.
## Examples
### Common operation
package main
import (
"fmt"
"io"
"os"
// "github.com/shenwei356/bio/seq"
"github.com/shenwei356/bio/seqio/fastx"
"github.com/shenwei356/xopen"
)
func main() {
// use buffered out stream for output
outfh, err := xopen.Wopen("-") // "-" for STDOUT
checkError(err)
defer outfh.Close()
// disable sequence validation could reduce time when reading large sequences
// seq.ValidateSeq = false
reader, err := fastx.NewDefaultReader("-")
checkError(err)
for {
record, err := reader.Read()
if err != nil {
if err == io.EOF {
break
}
checkError(err)
break
}
// fmt is slow for output, because it's not buffered
// fmt.Printf("%s", record.Format(0))
record.FormatToWriter(outfh, 0)
}
}
func checkError(err error) {
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
}
***Note that***, similar with `bytes.Buffer.Bytes()` method,
the current record will change after your another call of this method.
You may use `record.Clone()` to make a copy.
### Asynchronously parsing
`ChunkChan` asynchronously reads FASTA/Q records, and returns a channel of
Record Chunk, from which you can easily access the records.
`bufferSize` is the number of buffered chunks, and `chunkSize` is the size
of records in a chunk.
reader, err := fastx.NewDefaultReader(file)
checkError(err)
for chunk := range reader.ChunkChan(bufferSize, chunkSize) {
checkError(chunk.Err)
for _, record := range chunk.Data {
fmt.Print(record)
}
}
***Note that***, these's no need to clone the record by `record.Clone()` here.
### Custom alphabet and identifier regular expression
import (
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/bio/seqio/fastx"
)
reader, err := fastx.NewReader(seq.DNA, file, "^([^\s]+)\s?")
*/
package fastx
bio-0.13.3/seqio/fastx/empty.fx 0000664 0000000 0000000 00000000000 14573550650 0016311 0 ustar 00root root 0000000 0000000 bio-0.13.3/seqio/fastx/reader.go 0000775 0000000 0000000 00000036552 14573550650 0016435 0 ustar 00root root 0000000 0000000 package fastx
import (
"bytes"
"errors"
"fmt"
"io"
"regexp"
"sync"
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/xopen"
)
// ErrNotFASTXFormat means that the file is not FASTA/Q
var ErrNotFASTXFormat = errors.New("fastx: invalid FASTA/Q format")
// ErrBadFASTQFormat means bad fastq format
var ErrBadFASTQFormat = errors.New("fastx: bad fastq format")
// ErrUnequalSeqAndQual means unequal sequence and quality
var ErrUnequalSeqAndQual = errors.New("fastx: unequal sequence and quality")
// ErrNoContent means nothing in the file or stream
var ErrNoContent = errors.New("fastx: no content found")
var bufSize = 65536
var poolReader = &sync.Pool{New: func() interface{} {
t := &Reader{}
t.buf = make([]byte, bufSize)
t.buffer = bytes.NewBuffer(make([]byte, 0, defaultBytesBufferSize))
t.seqBuffer = bytes.NewBuffer(make([]byte, 0, defaultBytesBufferSize))
t.qualBuffer = bytes.NewBuffer(make([]byte, 0, defaultBytesBufferSize))
t.record = &Record{
ID: nil,
Name: nil,
Desc: nil,
Seq: &seq.Seq{}, // can't be nil
}
return t
}}
// Reader seamlessly parse both FASTA and FASTQ formats
type Reader struct {
fh *xopen.Reader // file handle, xopen is such a wonderful package
buf []byte // for store readed data from fh
r int
buffer *bytes.Buffer // buffer of a record
needMoreCheckOfBuf bool
lastByte byte
checkSeqType bool
lastPart bool
finished bool
firstseq bool // for guess alphabet by the first seq
delim byte
IsFastq bool // if the file is fastq format
t *seq.Alphabet // alphabet
IDRegexp *regexp.Regexp // regexp for parsing record id
head, seq, qual []byte
seqBuffer *bytes.Buffer
qualBuffer *bytes.Buffer
record *Record
// only for compatibility of empty files
Err error
}
func (fastxReader *Reader) Reset() {
n := bufSize - len(fastxReader.buf)
for i := 0; i < n; i++ {
fastxReader.buf = append(fastxReader.buf, 0)
}
fastxReader.r = 0
fastxReader.buffer.Reset()
fastxReader.needMoreCheckOfBuf = false
fastxReader.lastByte = 0
fastxReader.checkSeqType = true
fastxReader.lastPart = false
fastxReader.finished = false
fastxReader.firstseq = true
fastxReader.delim = 0
fastxReader.IsFastq = false
fastxReader.seqBuffer.Reset()
fastxReader.qualBuffer.Reset()
fastxReader.head = nil
fastxReader.seq = nil
fastxReader.qual = nil
fastxReader.Err = nil
}
// regexp for checking idRegexp string.
// The regular expression must contain "(" and ")" to capture matched ID
var reCheckIDregexpStr = regexp.MustCompile(`\(.+\)`)
// DefaultIDRegexp is the default ID parsing regular expression
var DefaultIDRegexp = `^(\S+)\s?`
var isUsingDefaultIDRegexp bool
// NewDefaultReader automaticlly recognizes sequence type and parses id with default manner
func NewDefaultReader(file string) (*Reader, error) {
return NewReader(nil, file, "")
}
var defaultBytesBufferSize = 10 << 20
// NewReader is constructor of FASTX Reader.
//
// Parameters:
//
// t sequence alphabet
// if nil is given, it will guess alphabet by the first record
// file file name, "-" for stdin
// idRegexp id parsing regular expression string, must contains "(" and ")" to capture matched ID
// "" for default value: `^([^\s]+)\s?`
// if record head does not match the idRegxp, whole name will be the id
//
// Please call reader.Close() afer using the records!!!
func NewReader(t *seq.Alphabet, file string, idRegexp string) (*Reader, error) {
var r *regexp.Regexp
if idRegexp == "" {
r = regexp.MustCompile(DefaultIDRegexp)
isUsingDefaultIDRegexp = true
} else {
if !reCheckIDregexpStr.MatchString(idRegexp) {
return nil, fmt.Errorf(`fastx: regular expression must contain "(" and ")" to capture matched ID. default: %s`, DefaultIDRegexp)
}
var err error
r, err = regexp.Compile(idRegexp)
if err != nil {
return nil, fmt.Errorf("fastx: fail to compile regexp: %s", idRegexp)
}
if idRegexp == DefaultIDRegexp {
isUsingDefaultIDRegexp = true
}
}
fh, err := xopen.Ropen(file)
if err != nil {
if err == xopen.ErrNoContent {
fastxReader := poolReader.Get().(*Reader)
fastxReader.Reset()
fastxReader.Err = io.EOF // so the first call of Read will return an io.EOF error.
return fastxReader, nil
}
return nil, fmt.Errorf("fastx: %s", err)
}
fastxReader := poolReader.Get().(*Reader)
fastxReader.Reset()
fastxReader.fh = fh
fastxReader.t = t
fastxReader.IDRegexp = r
return fastxReader, nil
}
// NewReaderFromIO is constructor of FASTX Reader.
//
// Parameters:
//
// t sequence alphabet
// if nil is given, it will guess alphabet by the first record
// file an io.Reader
// idRegexp id parsing regular expression string, must contains "(" and ")" to capture matched ID
// "" for default value: `^([^\s]+)\s?`
// if record head does not match the idRegxp, whole name will be the id
//
// Please call reader.Close() afer using the records!!!
func NewReaderFromIO(t *seq.Alphabet, ioReader io.Reader, idRegexp string) (*Reader, error) {
var r *regexp.Regexp
if idRegexp == "" {
r = regexp.MustCompile(DefaultIDRegexp)
isUsingDefaultIDRegexp = true
} else {
if !reCheckIDregexpStr.MatchString(idRegexp) {
return nil, fmt.Errorf(`fastx: regular expression must contain "(" and ")" to capture matched ID. default: %s`, DefaultIDRegexp)
}
var err error
r, err = regexp.Compile(idRegexp)
if err != nil {
return nil, fmt.Errorf("fastx: fail to compile regexp: %s", idRegexp)
}
if idRegexp == DefaultIDRegexp {
isUsingDefaultIDRegexp = true
}
}
fh, err := xopen.Buf(ioReader)
if err != nil {
panic(err)
}
fastxReader := poolReader.Get().(*Reader)
fastxReader.Reset()
fastxReader.fh = fh
fastxReader.t = t
fastxReader.IDRegexp = r
return fastxReader, nil
}
// Close cleans up everything, the most important thing is recyling the reader.
// Please do remember to calls this method!!!
func (fastxReader *Reader) Close() {
poolReader.Put(fastxReader)
}
// close closes the file handler
func (fastxReader *Reader) close() {
if fastxReader.fh != nil {
fastxReader.fh.Close()
}
}
// Read reads and return one FASTA/Q record.
// Note that, similar to bytes.Buffer.Bytes() method,
// the current record will change after your another call of this method.
// So, you could use record.Clone() to make a copy.
func (fastxReader *Reader) Read() (*Record, error) {
if fastxReader.lastPart && fastxReader.finished {
return nil, io.EOF
}
if fastxReader.Err != nil { // only for empty file
err := fastxReader.Err
return nil, err
}
var n int
var err error
var p []byte
for {
if !fastxReader.needMoreCheckOfBuf && !fastxReader.lastPart {
n, err = fastxReader.fh.Read(fastxReader.buf)
if err != nil {
if err == io.EOF {
fastxReader.lastPart = true
} else {
return nil, err
}
} else if n == 0 {
fastxReader.close()
return nil, io.ErrUnexpectedEOF
}
// last part of file OR just because reader not fulfill the buf,
// like reading from stdin
if n < len(fastxReader.buf) {
// fastxReader.lastPart = true
fastxReader.buf = fastxReader.buf[0:n] // very important!
}
fastxReader.r = 0 /// TO CHECK
}
// check seq type via the first non-empty charator, run for onece
if fastxReader.checkSeqType {
pn := 0
FORCHECK:
for i := range fastxReader.buf {
switch fastxReader.buf[i] {
case '>':
fastxReader.checkSeqType = false
fastxReader.IsFastq = false
fastxReader.delim = '>'
fastxReader.r = i + 1
break FORCHECK
case '@':
fastxReader.IsFastq = true
fastxReader.delim = '@'
fastxReader.r = i + 1
break FORCHECK
case '\n': // allow some lines
pn++
if pn > 100 {
if i > 10240 { // ErrNotFASTXFormat
fastxReader.close()
return nil, ErrNotFASTXFormat
}
}
// break FORCHECK
default: // not typical FASTA/Q
// if i > 10240 || fastxReader.lastPart { // ErrNotFASTXFormat
fastxReader.close()
return nil, ErrNotFASTXFormat
// }
}
}
fastxReader.checkSeqType = false
}
var shorterQual bool
var i int
FORSEARCH:
for {
if i = bytes.IndexByte(fastxReader.buf[fastxReader.r:], fastxReader.delim); i >= 0 {
if i > 0 {
fastxReader.lastByte = fastxReader.buf[fastxReader.r+i-1]
} else {
p = fastxReader.buffer.Bytes()
if len(p) == 0 {
fastxReader.lastByte = '\x00'
} else {
fastxReader.lastByte = p[len(p)-1]
}
}
if fastxReader.lastByte == '\n' { // yes!
if i > 0 {
fastxReader.buffer.Write(dropCR(fastxReader.buf[fastxReader.r : fastxReader.r+i-1]))
} else {
fastxReader.buffer.WriteByte('\n')
}
// we have to avoid the case of quality line starting with "@"
shorterQual, err = fastxReader.parseRecord()
if fastxReader.IsFastq && err != nil && err == ErrUnequalSeqAndQual {
if shorterQual {
fastxReader.buffer.WriteByte('\n')
fastxReader.buffer.WriteByte(fastxReader.delim)
fastxReader.needMoreCheckOfBuf = true
fastxReader.r += i + 1
continue FORSEARCH
}
fastxReader.close()
return nil, ErrBadFASTQFormat
}
fastxReader.buffer.Reset()
fastxReader.needMoreCheckOfBuf = true
fastxReader.r += i + 1
return fastxReader.record, nil
}
// inline >/@
fastxReader.buffer.Write(fastxReader.buf[fastxReader.r : fastxReader.r+i+1])
fastxReader.r += i + 1
fastxReader.needMoreCheckOfBuf = true
continue FORSEARCH
}
fastxReader.buffer.Write(fastxReader.buf[fastxReader.r:])
if fastxReader.lastPart {
_, err = fastxReader.parseRecord()
if err != nil { // no any chance
fastxReader.close()
return nil, err
}
fastxReader.buffer.Reset()
fastxReader.close()
fastxReader.finished = true
return fastxReader.record, nil
}
fastxReader.needMoreCheckOfBuf = false
break FORSEARCH
}
}
}
// parseRecord parse a FASTA/Q record from the fastxReader.buffer
func (fastxReader *Reader) parseRecord() (bool, error) {
fastxReader.seqBuffer.Reset()
if fastxReader.IsFastq {
fastxReader.qualBuffer.Reset()
}
var p = fastxReader.buffer.Bytes()
if j := bytes.IndexByte(p, '\n'); j > 0 {
fastxReader.head = dropCR(p[0:j])
r := j + 1
if !fastxReader.IsFastq { // FASTA
for {
if k := bytes.IndexByte(p[r:], '\n'); k >= 0 {
fastxReader.seqBuffer.Write(dropCR(p[r : r+k]))
r += k + 1
continue
}
fastxReader.seqBuffer.Write(dropCR(p[r:]))
break
}
fastxReader.seq = fastxReader.seqBuffer.Bytes()
} else { // FASTQ
var isQual bool
for {
if k := bytes.IndexByte(p[r:], '\n'); k >= 0 {
if k > 0 && p[r] == '+' && !isQual {
isQual = true
} else if isQual {
fastxReader.qualBuffer.Write(dropCR(p[r : r+k]))
} else {
fastxReader.seqBuffer.Write(dropCR(p[r : r+k]))
}
r += k + 1
continue
}
if isQual {
fastxReader.qualBuffer.Write(dropCR(p[r:]))
}
break
}
// may be the case of quality line starts with "@"
if fastxReader.seqBuffer.Len() != fastxReader.qualBuffer.Len() {
return fastxReader.seqBuffer.Len() > fastxReader.qualBuffer.Len(), ErrUnequalSeqAndQual
}
fastxReader.seq = fastxReader.seqBuffer.Bytes()
fastxReader.qual = fastxReader.qualBuffer.Bytes()
}
} else {
fastxReader.head = dropCR(dropLF(p))
fastxReader.seq = []byte{}
fastxReader.qual = []byte{}
}
// guess alphabet
if fastxReader.firstseq {
if fastxReader.t == nil {
fastxReader.t = seq.GuessAlphabetLessConservatively(fastxReader.seq)
}
fastxReader.firstseq = false
}
if len(fastxReader.head) == 0 && len(fastxReader.seq) == 0 {
return false, io.EOF
}
var err error
// new record
if fastxReader.IsFastq { // fastq
fastxReader.record.Seq.Alphabet = fastxReader.t
fastxReader.record.ID, fastxReader.record.Desc = parseHeadIDAndDesc(fastxReader.IDRegexp, fastxReader.head)
fastxReader.record.Name = fastxReader.head
fastxReader.record.Seq.Seq = fastxReader.seq
fastxReader.record.Seq.Qual = fastxReader.qual
if seq.ValidateSeq {
err = fastxReader.t.IsValid(fastxReader.seq)
}
if len(fastxReader.seq) != len(fastxReader.qual) {
err = fmt.Errorf("seq: unmatched length of sequence (%d) and quality (%d)",
len(fastxReader.seq), len(fastxReader.qual))
}
} else { // fasta
fastxReader.record.Seq.Alphabet = fastxReader.t
fastxReader.record.ID, fastxReader.record.Desc = parseHeadIDAndDesc(fastxReader.IDRegexp, fastxReader.head)
fastxReader.record.Name = fastxReader.head
fastxReader.record.Seq.Seq = fastxReader.seq
if seq.ValidateSeq {
err = fastxReader.t.IsValid(fastxReader.seq)
}
}
return false, err
}
// ParseHeadID parse ID from head by IDRegexp. not used.
func ParseHeadID(idRegexp *regexp.Regexp, head []byte) []byte {
found := idRegexp.FindSubmatch(head)
if found == nil { // not match
return head
}
return found[1]
}
var emptyByteSlice = []byte{}
func parseHeadIDAndDesc(idRegexp *regexp.Regexp, head []byte) ([]byte, []byte) {
if isUsingDefaultIDRegexp {
if i := bytes.IndexByte(head, ' '); i > 0 {
e := len(head)
j := i + 1
for ; j < e; j++ {
if head[j] == ' ' || head[j] == '\t' {
j++
} else {
break
}
}
if j >= e {
return head[0:i], emptyByteSlice
}
return head[0:i], head[j:]
}
if i := bytes.IndexByte(head, '\t'); i > 0 {
e := len(head)
j := i + 1
for ; j < e; j++ {
if head[j] == ' ' || head[j] == '\t' {
j++
} else {
break
}
}
if j >= e {
return head[0:i], emptyByteSlice
}
return head[0:i], head[j:]
}
return head, emptyByteSlice
}
found := idRegexp.FindSubmatch(head)
if found == nil { // not match
return head, emptyByteSlice
}
return found[1], emptyByteSlice
}
// Alphabet returns Alphabet of the file
func (fastxReader *Reader) Alphabet() *seq.Alphabet {
if fastxReader.t == nil {
return seq.Unlimit
}
return fastxReader.t
}
func dropCR(data []byte) []byte {
if len(data) > 0 && data[len(data)-1] == '\r' {
return data[0 : len(data)-1]
}
return data
}
func dropLF(data []byte) []byte {
if len(data) > 0 && data[len(data)-1] == '\n' {
return data[0 : len(data)-1]
}
return data
}
// -------------------------------------------------
// RecordChunk is chunk for records
type RecordChunk struct {
ID uint64
Data []*Record
Err error
}
// ChunkChan asynchronously reads FASTA/Q records, and returns a channel of
// Record Chunk, from which you can easily access the records.
// bufferSize is the number of buffered chunks, and chunkSize is the size
// of records in a chunk.
func (fastxReader *Reader) ChunkChan(bufferSize int, chunkSize int) chan RecordChunk {
var ch chan RecordChunk
if bufferSize <= 0 {
ch = make(chan RecordChunk)
} else {
ch = make(chan RecordChunk, bufferSize)
}
if chunkSize < 1 {
chunkSize = 1
}
go func() {
var i int
var id uint64
chunkData := make([]*Record, chunkSize)
for {
record, err := fastxReader.Read()
if err != nil {
if err == io.EOF {
if i == 0 { // no any seqs
close(ch)
return
}
break
}
ch <- RecordChunk{id, chunkData[0:i], err}
close(ch)
return
}
chunkData[i] = record.Clone()
i++
if i == chunkSize {
ch <- RecordChunk{id, chunkData[0:i], nil}
id++
i = 0
chunkData = make([]*Record, chunkSize)
}
}
ch <- RecordChunk{id, chunkData[0:i], nil}
close(ch)
}()
return ch
}
bio-0.13.3/seqio/fastx/reader_test.go 0000775 0000000 0000000 00000006704 14573550650 0017470 0 ustar 00root root 0000000 0000000 package fastx
import (
// "fmt"
"io"
"testing"
)
func TestFastaReader2(t *testing.T) {
file := "test.fa"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
for {
_, err := reader.Read()
if err != nil {
if err == io.EOF {
break
}
t.Error(err)
break
}
// fmt.Print(record)
}
}
func TestFastaReader3(t *testing.T) {
file := "test.fa"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
for chunk := range reader.ChunkChan(0, 1) {
if chunk.Err != nil {
t.Error(chunk.Err)
}
// for _, record := range chunk.Data {
// // fmt.Print(record)
// }
}
}
func TestFastqReadern(t *testing.T) {
file := "test.fq"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
for {
_, err := reader.Read()
if err != nil {
if err == io.EOF {
break
}
t.Error(err)
break
}
// fmt.Print(record)
}
}
// -----------------------------
func TestFastaReader(t *testing.T) {
file := "test.fa"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
n := 0
for chunk := range reader.ChunkChan(0, 1) {
if chunk.Err != nil {
t.Error(chunk.Err)
}
n += len(chunk.Data)
// for _, record := range chunk.Data {
// fmt.Println(record)
// }
}
if n != 6 {
t.Errorf("seq number mismatch %d != %d", 6, n)
}
}
func TestFastqReader(t *testing.T) {
file := "test.fq"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
n := 0
for chunk := range reader.ChunkChan(0, 1) {
if chunk.Err != nil {
t.Error(chunk.Err)
}
n += len(chunk.Data)
// for _, record := range chunk.Data {
// fmt.Println(record)
// }
}
if n != 8 {
t.Errorf("seq number mismatch %d != %d", 8, n)
}
}
func TestFastqReader2(t *testing.T) {
file := "test2.fq"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
n := 0
for chunk := range reader.ChunkChan(0, 1) {
if chunk.Err != nil {
t.Error(chunk.Err)
}
n += len(chunk.Data)
// for _, record := range chunk.Data {
// fmt.Println(record)
// }
}
if n != 5 {
t.Errorf("seq number mismatch %d != %d", 5, n)
}
}
func TestFastqReader3(t *testing.T) {
file := "test3.fq"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
n := 0
l := -1
for chunk := range reader.ChunkChan(0, 1) {
if chunk.Err != nil {
t.Error(chunk.Err)
}
n += len(chunk.Data)
for _, record := range chunk.Data {
// fmt.Println(record)
if l == -1 {
l = len(record.Seq.Seq)
} else {
if l != len(record.Seq.Seq) {
t.Errorf("parse error")
return
}
}
}
}
if n != 3 {
t.Errorf("seq number mismatch %d != %d", 5, n)
}
}
func TestBlankFile(t *testing.T) {
file := "blank.fx"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
for chunk := range reader.ChunkChan(0, 1) {
if chunk.Err != nil {
if chunk.Err != ErrNotFASTXFormat {
t.Error(chunk.Err)
}
}
}
}
func TestBlankFile2(t *testing.T) {
file := "blank1.fx"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
for chunk := range reader.ChunkChan(0, 1) {
// should not reach here
t.Errorf("should not reach here. error: %s", chunk.Err)
return
}
}
func TestEmptyFile(t *testing.T) {
file := "empty.fx"
reader, err := NewDefaultReader(file)
if err != nil {
t.Error(err)
}
for chunk := range reader.ChunkChan(0, 1) {
// should not reach here
t.Errorf("should not reach here. error: %s", chunk.Err)
return
}
}
bio-0.13.3/seqio/fastx/records.go 0000775 0000000 0000000 00000011025 14573550650 0016620 0 ustar 00root root 0000000 0000000 package fastx
import (
"bytes"
"fmt"
"sync"
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/xopen"
)
// Record is a struct for FASTA/Q
type Record struct {
ID []byte // id
Name []byte // full name
Desc []byte // Description
Seq *seq.Seq // seq
}
// Clone of a Record
func (record *Record) Clone() *Record {
return &Record{
[]byte(string(record.ID)),
[]byte(string(record.Name)),
[]byte(string(record.Desc)),
record.Seq.Clone(),
}
}
func (record *Record) String() string {
return string(record.Format(60))
}
// NewRecord is constructor of type Record for FASTA
func NewRecord(t *seq.Alphabet, id, name, desc, s []byte) (*Record, error) {
seq, err := seq.NewSeq(t, s)
if err != nil {
return nil, fmt.Errorf("error when parsing seq: %s (%s)", id, err)
}
return &Record{id, name, desc, seq}, nil
}
// NewRecordWithoutValidation is constructor of type Record for FASTA
// without validation of the sequence
func NewRecordWithoutValidation(t *seq.Alphabet, id, name, desc, s []byte) (*Record, error) {
seq, err := seq.NewSeqWithoutValidation(t, s)
if err != nil {
return nil, err
}
return &Record{id, name, desc, seq}, nil
}
// NewRecordWithSeq is constructor of type Record
// for FASTA with a existed seq.Seq object
func NewRecordWithSeq(id, name, desc []byte, s *seq.Seq) (*Record, error) {
return &Record{id, name, desc, s}, nil
}
// NewRecordWithQual is constructor of type Record for FASTQ
func NewRecordWithQual(t *seq.Alphabet, id, name, desc, s, q []byte) (*Record, error) {
seq, err := seq.NewSeqWithQual(t, s, q)
if err != nil {
return nil, fmt.Errorf("error when parsing seq: %s (%s)", id, err)
}
return &Record{id, name, desc, seq}, nil
}
// NewRecordWithQualWithoutValidation is constructor of type Record for FASTQ
func NewRecordWithQualWithoutValidation(t *seq.Alphabet, id, name, desc, s, q []byte) (*Record, error) {
seq, err := seq.NewSeqWithQualWithoutValidation(t, s, q)
if err != nil {
return nil, err
}
return &Record{id, name, desc, seq}, nil
}
// ForcelyOutputFastq means outputing record as fastq even if it has no quality (zero-length fastq)
var ForcelyOutputFastq bool
// Format returns formated (wrapped with fixed length of) sequence record
func (record *Record) Format(width int) []byte {
var buf bytes.Buffer
if len(record.Seq.Qual) > 0 || ForcelyOutputFastq {
buf.Write(_mark_fastq)
buf.Write(record.Name)
buf.Write(_mark_newline)
buf.Write(record.Seq.Seq)
buf.Write(_mark_newline_plus_newline)
buf.Write(record.Seq.Qual)
buf.Write(_mark_newline)
return buf.Bytes()
}
buf.Write(_mark_fasta)
buf.Write(record.Name)
buf.Write(_mark_newline)
if width < 1 {
buf.Write(record.Seq.Seq)
} else {
var text []byte
buffer := poolBuffer.Get().(*bytes.Buffer)
text, buffer = wrapByteSlice(record.Seq.Seq, width, buffer)
buf.Write(text)
poolBuffer.Put(buffer)
}
buf.Write(_mark_newline)
return buf.Bytes()
}
// FormatToWriter formats and directly writes to writer
func (record *Record) FormatToWriter(outfh *xopen.Writer, width int) {
if len(record.Seq.Qual) > 0 || ForcelyOutputFastq {
outfh.Write(_mark_fastq)
outfh.Write(record.Name)
outfh.Write(_mark_newline)
outfh.Write(record.Seq.Seq)
outfh.Write(_mark_newline_plus_newline)
outfh.Write(record.Seq.Qual)
outfh.Write(_mark_newline)
return
}
outfh.Write(_mark_fasta)
outfh.Write(record.Name)
outfh.Write(_mark_newline)
if width < 1 {
outfh.Write(record.Seq.Seq)
} else {
var text []byte
buffer := poolBuffer.Get().(*bytes.Buffer)
text, buffer = wrapByteSlice(record.Seq.Seq, width, buffer)
outfh.Write(text)
poolBuffer.Put(buffer)
}
outfh.Write(_mark_newline)
}
// It's unsafe for concurrency
// var buffer *bytes.Buffer
var poolBuffer = &sync.Pool{New: func() interface{} {
return bytes.NewBuffer(make([]byte, 0, 1024))
}}
var _mark_fasta = []byte{'>'}
var _mark_fastq = []byte{'@'}
var _mark_newline_plus_newline = []byte{'\n', '+', '\n'}
var _mark_newline = []byte{'\n'}
func wrapByteSlice(s []byte, width int, buffer *bytes.Buffer) ([]byte, *bytes.Buffer) {
if width < 1 {
return s, buffer
}
l := len(s)
if l == 0 {
return s, buffer
}
var lines int
if l%width == 0 {
lines = l/width - 1
} else {
lines = int(l / width)
}
if buffer == nil {
buffer = bytes.NewBuffer(make([]byte, 0, l+lines))
} else {
buffer.Reset()
}
var start, end int
for i := 0; i <= lines; i++ {
start = i * width
end = (i + 1) * width
if end > l {
end = l
}
buffer.Write(s[start:end])
if i < lines {
buffer.Write(_mark_newline)
}
}
return buffer.Bytes(), buffer
}
bio-0.13.3/seqio/fastx/test.fa 0000775 0000000 0000000 00000002057 14573550650 0016124 0 ustar 00root root 0000000 0000000 >test ab > cd
UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAAC
UAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA
>cel-lin-4 MI0000002 Caenorhabditis elegans lin-4 stem-loop
AUGCUUCCGGCCUGUUCCCUGAGACCUCAAGUGUGAGUGUACUAUUGAUGCUUCACACCU
GGGCUCUCCGGGUACCAGGACGGUUUGAGCAGAU
>cel-mir-46 MI0000017 Caenorhabditis elegans miR-46 stem-loop
CUGAGGUGAAGCUGAAGAGAGCCGUCUAUUGACAGUUCAAGACCACGAGUCGUUGUGUGC
GGUAUCAGGAAGUGGGCAACCGCCUCCAGACGCCGAGAAGCUGGUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAA
CAAGGUUUCCGUAGGUGAACUGCGGA
>record with no sequence
>U51103.1.1480 Bacteria;Proteobacteria;Gammaproteobacteria;Xanthomonadales;Xanthomonadaceae;Thermomonas;denitrifying Fe-oxidizing bacterium
UGGCGGCAGGCCUAACACAUGCAAGUCGAACGGCAGCACAGCAGAGCUUGCUCUGUGGGUGGCGAGUGGCGGACGGGUGA
GGAAUACAUGGGAAUCUGCCCAGUCGUGGGGGAUAACGUAUGGAAACGUACGCUAAUACCGCAUGCGCCCUUUGGGGGAA
>cel-mir-46 MI0000017 Caenorhabditis elegans miR-46 stem-loop
CUGAGGUGAAGCUGAAGAGAGCCGUCUAUUGACAGUUCAAGACCACGAGUCGUUGUGUGC
GGUAUCAGGAAGUGGGCAACCGCCUCCAGACGCCGAGAAGCUGGUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAA
CAAGGUUUCCGUAGGUGAACUGCGGA
bio-0.13.3/seqio/fastx/test.fq 0000664 0000000 0000000 00000010030 14573550650 0016127 0 ustar 00root root 0000000 0000000 @HWI-D00523:240:HF3WGBCXX:1:1101:2574:2226 1:N:0:CTGTAG
TGAGGAATATTGGTCAATGGGCGCGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTACGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTGAGGCACGTGTGCCTTTTTGTATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGT
+
HIHIIIIIHIIHGHHIHHIIIIIIIIIIIIIIIHHIIIIIHHIHIIIIIGIHIIIIHHHHHHGHIHIIIIIIIIIIIGHIIIIIGHIIIIHIIHIHHIIIIHIHHIIIIIIIGIIIIIIIHIIIIIGHIIIIHIIIH?DGHEEGHIIIIIIIIIIIHIIHIIIHHIIHIHHIHCHHIIHGIHHHHHHHHHHHHHHDEH<@H-@CDD>:E?@GHEF-@E:@H+@-@@
@HWI-D00523:240:HF3WGBCXX:1:1101:15680:15180 1:N:0:CTGTAG
TGAGGAATATTGGTCAATGGTCGGGAGACTGAACCAGCCAAGCCGCGTGAGGGAGGAAGGTACAGAGTATCGTAAACCTCTTTTGTCAGGGAACAAAGGCGGGGACGTGTCCCCGGATGAGTGTACCTGAAGAAAAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTGTAAAGGGTGCGCAGGCGGT
+
@@EE@@HHIIIIICHHIIHIHHHHHHHHHDEH<@H-@CDD>:E?@GHEF-@E:@H+@-@@
@HWI-D00523:240:HF3WGBCXX:1:1101:3159:2162 1:N:0:CTGTAG
TGAGGAATATTGGTCAATGGTCGGGAGACTGAACCAGCCAAGCCGCGTGAGGGAGGAAGG
TACAGAGTATCGTAAACCTCTTTTGTCAGGGGACAAAGACTGGGACGCGTCCCCGGATGA
GTTTACCTGAAGATAAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGA
TGCGAGCGTTATTCGGATTTCTTGGATTTAAAGGGTGCGCAGGCGGT
+
D1<DEHH>HHAHIIGGGII@CFFHGDFHI;:?FGB6@AGIIIGH=@?EEE3=B;?BCFEC>BB@?B8=B9>@@9?A3>@09<5>+8?><<)5@+@@=EA::??C6',-(5::,5350077<<&8(3+3(+++:::ABA@>?9@@<>BB#########
@HWI-1KL131:72:C1BH9ACXX:1:1101:1364:2370 1:N:0:AGGCAGAACTCTCTAT
GAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGGTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATAGAAGG
+
=@@DD3B3A:2A;AFBBG9C;+28??;31?@HG6;@>?D88@7@-:ED>CE?>'3;:?C@;533:>>8?################################
bio-0.13.3/seqio/fastx/test4.fa 0000664 0000000 0000000 00000000052 14573550650 0016176 0 ustar 00root root 0000000 0000000 >a
ATC
>b
>123
ATCGN
>abcdefg
ATCGN
GCCTN
bio-0.13.3/seqio/fastx/util.go 0000775 0000000 0000000 00000004332 14573550650 0016137 0 ustar 00root root 0000000 0000000 package fastx
import (
"io"
"github.com/shenwei356/bio/seq"
)
// GetSeqNames returns the names of a fasta/q file
func GetSeqNames(file string) ([]string, error) {
names := []string{}
seq.ValidateSeq = false
reader, err := NewDefaultReader(file)
if err != nil {
return nil, nil
}
for {
record, err := reader.Read()
if err != nil {
if err == io.EOF {
break
}
return nil, err
}
names = append(names, string(record.Name))
}
return names, nil
}
// GetSeqNumber returns the sequences number of FASTA/Q files
func GetSeqNumber(file string) (int, error) {
n := 0
seq.ValidateSeq = false
reader, err := NewDefaultReader(file)
if err != nil {
return 0, nil
}
for {
_, err := reader.Read()
if err != nil {
if err == io.EOF {
break
}
return 0, err
}
n++
}
return n, nil
}
// GetSeqs return fastx records of a file.
// when alphabet is nil or seq.Unlimit, it will automaticlly detect the alphabet.
// when idRegexp is "", default idRegexp ( ^([^\s]+)\s? ) will be used.
func GetSeqs(file string, alphabet *seq.Alphabet, bufferSize int, chunkSize int, idRegexp string) ([]*Record, error) {
records := []*Record{}
reader, err := NewReader(alphabet, file, idRegexp)
if err != nil {
return records, err
}
for chunk := range reader.ChunkChan(bufferSize, chunkSize) {
if err != nil {
return records, err
}
records = append(records, chunk.Data...)
}
return records, nil
}
// GetSeqsMap returns all seqs as a map for fasta file
func GetSeqsMap(file string, alphabet *seq.Alphabet, bufferSize int, chunkSize int, idRegexp string) (map[string]*Record, error) {
m := make(map[string]*Record)
records, err := GetSeqs(file, alphabet, bufferSize, chunkSize, idRegexp)
if err != nil {
return m, err
}
for _, record := range records {
m[string(record.Name)] = record
}
return m, nil
}
// GuessAlphabet guess the alphabet of the file by the first maxLen bases
func GuessAlphabet(file string) (*seq.Alphabet, bool, error) {
reader, err := NewDefaultReader(file)
if err != nil {
return nil, false, err
}
_, err = reader.Read()
if err != nil {
if err == io.EOF {
return reader.Alphabet(), false, io.EOF
}
return nil, false, err
}
return reader.Alphabet(), reader.IsFastq, nil
}
bio-0.13.3/sketches/ 0000775 0000000 0000000 00000000000 14573550650 0014172 5 ustar 00root root 0000000 0000000 bio-0.13.3/sketches/README.md 0000775 0000000 0000000 00000003631 14573550650 0015457 0 ustar 00root root 0000000 0000000 # sketches
[](https://pkg.go.dev/github.com/shenwei356/bio/sketches)
This package provides iterators for k-mer and k-mer sketches
([Minimizer](https://academic.oup.com/bioinformatics/article/20/18/3363/202143),
[Scaled MinHash](https://f1000research.com/articles/8-1006),
[Closed Syncmers](https://peerj.com/articles/10805/)).
K-mers are either encoded (k<=32) or hashed (arbitrary k, using [ntHash](https://github.com/will-rowe/nthash)) into `uint64`.
Related projects:
- [kmers](https://github.com/shenwei356/kmers) provides manipulations for bit-packed k-mers (k<=32, encoded in `uint64`).
- [kmcp](https://github.com/shenwei356/kmcp) uses this package.
## Benchmark
CPU: AMD Ryzen 7 2700X Eight-Core Processor, 3.7 GHz
$ go test . -bench=Bench* -benchmem \
| grep Bench \
| perl -pe 's/\s\s+/\t/g' \
| csvtk cut -Ht -f 1,3-5 \
| csvtk add-header -t -n test,time,memory,allocs \
| csvtk pretty -t -r
test time memory allocs
------------------------------------------ ------------ -------- -----------
BenchmarkKmerIterator/1.00_KB-16 11445 ns/op 0 B/op 0 allocs/op
BenchmarkHashIterator/1.00_KB-16 7974 ns/op 24 B/op 1 allocs/op
BenchmarkSimHashIterator/1.00_KB-16 79477 ns/op 48 B/op 1 allocs/op
BenchmarkProteinIterator/1.00_KB-16 17852 ns/op 432 B/op 2 allocs/op
BenchmarkMinimizerSketch/1.00_KB-16 56071 ns/op 48 B/op 2 allocs/op
BenchmarkSyncmerSketch/1.00_KB-16 101310 ns/op 977 B/op 7 allocs/op
BenchmarkProteinMinimizerSketch/1.00_KB-16 29914 ns/op 736 B/op 5 allocs/op
## History
This package was originally maintained in [unikmer](https://github.com/shenwei356/unikmer).
bio-0.13.3/sketches/iterator-protein.go 0000664 0000000 0000000 00000005120 14573550650 0020026 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
import (
"sync"
"github.com/shenwei356/bio/seq"
"github.com/zeebo/wyhash"
)
var poolProteinIterator = &sync.Pool{New: func() interface{} {
return &ProteinIterator{}
}}
// ProteinIterator is a iterator for protein sequence.
type ProteinIterator struct {
s0 *seq.Seq // only used for KmerProteinIterator
s *seq.Seq // amino acid
k int
finished bool
end int
idx int
}
// NewProteinIterator returns an iterator for hash of amino acids
func NewProteinIterator(s *seq.Seq, k int, codonTable int, frame int) (*ProteinIterator, error) {
if k < 1 {
return nil, ErrInvalidK
}
if len(s.Seq) < k*3 {
return nil, ErrShortSeq
}
// iter := &ProteinIterator{s0: s, k: k}
iter := poolProteinIterator.Get().(*ProteinIterator)
iter.s0 = s
iter.k = k
iter.finished = false
iter.idx = 0
var err error
if s.Alphabet != seq.Protein {
iter.s, err = s.Translate(codonTable, frame, false, false, true, false)
if err != nil {
return nil, err
}
} else {
iter.s = s
}
iter.end = len(iter.s.Seq) - k
return iter, nil
}
// Next return's a hash
func (iter *ProteinIterator) Next() (code uint64, ok bool) {
if iter.finished {
return 0, false
}
if iter.idx > iter.end {
iter.finished = true
poolProteinIterator.Put(iter)
return 0, false
}
code = wyhash.Hash(iter.s.Seq[iter.idx:iter.idx+iter.k], 1)
iter.idx++
return code, true
}
// Index returns current 0-baesd index.
func (iter *ProteinIterator) Index() int {
return iter.idx - 1
}
bio-0.13.3/sketches/iterator-protein_test.go 0000664 0000000 0000000 00000003633 14573550650 0021074 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
import (
"testing"
"github.com/shenwei356/bio/seq"
)
func TestProteinIterator(t *testing.T) {
_s := "AAGTTTGAATCATTCAACTATCTAGTTTTCAGAGAACAATGTTCTCTAAAGAATAGAAAAGAGTCATTGTGCGGTGATGATGGCGGGAAGGATCCACCTG"
sequence, err := seq.NewSeq(seq.DNA, []byte(_s))
if err != nil {
t.Errorf("fail to create sequence: %s", _s)
}
k := 10
iter, err := NewProteinIterator(sequence, k, 1, 1)
if err != nil {
t.Errorf("fail to create aa iter rator")
}
var code uint64
var ok bool
// var idx int
codes := make([]uint64, 0, 1024)
for {
code, ok = iter.Next()
if !ok {
break
}
// idx = iter.Index()
// fmt.Printf("aa: %d-%s, %d\n", idx, iter.s.Seq[idx:idx+k], code)
codes = append(codes, code)
}
if len(codes) != len(_s)/3-k+1 {
t.Errorf("k-mer hashes number error")
}
}
bio-0.13.3/sketches/iterator.go 0000664 0000000 0000000 00000066552 14573550650 0016370 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
import (
"errors"
"fmt"
"math"
"sync"
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/kmers"
"github.com/will-rowe/nthash"
)
// ErrInvalidK means k < 1.
var ErrInvalidK = fmt.Errorf("sketches: invalid k-mer size")
// ErrEmptySeq sequence is empty.
var ErrEmptySeq = fmt.Errorf("sketches: empty sequence")
// ErrShortSeq means the sequence is shorter than k
var ErrShortSeq = fmt.Errorf("sketches: sequence too short")
// ErrIllegalBase means that base beyond IUPAC symbols are detected.
var ErrIllegalBase = errors.New("sketches: illegal base")
// ErrKTooLarge means that the k-mer size is too large.
var ErrKTooLarge = fmt.Errorf("sketches: k-mer size is too large")
// ErrInvalidM means that the m-mer size is too large or too small, should be in range of [4, k].
var ErrInvalidM = fmt.Errorf("sketches: invalid m-mer size, should be in range of [4, k]")
// ErrInvalidScale means
var ErrInvalidScale = fmt.Errorf("sketches: invalid scale, should be in range of [1, k-m+1]")
var poolIterator = &sync.Pool{New: func() interface{} {
return &Iterator{}
}}
// Iterator is a kmer code (k<=32) or hash iterator.
type Iterator struct {
s *seq.Seq // only used for KmerIterator
k int
kUint uint // uint(k)
kP1 int // k -1
kP1Uint uint // uint(k-1)
canonical bool
circular bool
hash bool
finished bool
revcomStrand bool
idx int
// for KmerIterator
length int
end, e int
first bool
kmer []byte
codeBase uint64
preCode uint64
preCodeRC uint64
codeRC uint64
mask1 uint64 // (1<<(kP1Uint*2))-1
mask2 uint // iter.kP1Uint*2
// for HashIterator
hasher *nthash.NTHi
// for SimHash
simhash bool
m int // size of m-mer
em int // end of idxJ in current k-mer
hashes []uint64 // cycle buffer of previous hashes of m-mer
sum [64]int16 // the vector
nPosHash int16 // number of vector value > 0
nThsld int16 // the threshold to decide should a vector value be 1 (x >= nThsld) or not
idxJ int // tmp index
preHashI int // index of the m-mer just getting out of the current k-mer
preHash uint64 //
_hash uint64 // ntHash
fracMinHash bool // scale > 1
maxHash uint64 // the max hash value for a scale, i.e. max uint64 / scale
}
// NewSimHashIterator returns a SimHash Iterator. Main parameters:
//
// k: k-mer size.
// m: size of m-mer in a k-mer. range: [4, k]
// scale: scale of FracMinHash of m-mers. range: [1, k-m+1]
func NewSimHashIterator(s *seq.Seq, k int, m int, scale int, canonical bool, circular bool) (*Iterator, error) {
if k < 1 {
return nil, ErrInvalidK
}
if k >= 65535 {
return nil, ErrKTooLarge
}
if m < 4 || m > k {
return nil, ErrInvalidM
}
if scale < 1 || scale > k-m+1 {
return nil, ErrInvalidScale
}
if len(s.Seq) < k {
return nil, ErrShortSeq
}
var s2 *seq.Seq
if circular {
s2 = s.Clone() // do not edit original sequence
s2.Seq = append(s2.Seq, s.Seq[0:k-1]...)
} else {
s2 = s
}
// iter := &Iterator{s: s2, k: k, canonical: canonical, circular: circular}
iter := poolIterator.Get().(*Iterator)
iter.s = s2
iter.k = k
iter.canonical = canonical
iter.circular = circular
iter.finished = false
iter.revcomStrand = false
iter.idx = 0
iter.length = len(s2.Seq)
iter.end = iter.length - k + 1
iter.kUint = uint(k)
iter.kP1 = k - 1
iter.kP1Uint = uint(k - 1)
iter.first = true
var err error
iter.hasher, err = nthash.NewHasher(&s2.Seq, uint(m))
if err != nil {
return nil, err
}
for i := 0; i < 64; i++ {
iter.sum[i] = 0
}
iter.nPosHash = 0
iter.simhash = true
iter.m = m
iter.em = iter.k - iter.m
iter.nThsld = 0 // int16((float64(iter.k-iter.m+1) + 1) / float64(2))
if len(iter.hashes) >= iter.k-iter.m+1 { // resuse objects
iter.hashes = iter.hashes[0 : iter.k-iter.m+1]
} else {
iter.hashes = make([]uint64, iter.k-iter.m+1)
}
iter.preHashI = 0
iter.idxJ = 0
iter.fracMinHash = scale > 1
if iter.fracMinHash {
iter.maxHash = math.MaxUint64 / uint64(scale)
} else {
iter.maxHash = math.MaxUint64
}
return iter, nil
}
// NextSimHash returns next SimHash.
func (iter *Iterator) NextSimHash() (code uint64, ok bool) {
if iter.finished {
return 0, false
}
if iter.idx == iter.end {
iter.finished = true
poolIterator.Put(iter)
return 0, false
}
if !iter.first {
// subtract the previous hash, which is out of the window of current k-mer
iter.preHash = iter.hashes[iter.preHashI]
// fmt.Printf("[%d] prevHashI: %d\n", iter.idx, iter.preHashI)
if iter.preHash > 0 {
iter.nPosHash--
iter.sum[0] -= int16(iter.preHash >> 63 & 1)
iter.sum[1] -= int16(iter.preHash >> 62 & 1)
iter.sum[2] -= int16(iter.preHash >> 61 & 1)
iter.sum[3] -= int16(iter.preHash >> 60 & 1)
iter.sum[4] -= int16(iter.preHash >> 59 & 1)
iter.sum[5] -= int16(iter.preHash >> 58 & 1)
iter.sum[6] -= int16(iter.preHash >> 57 & 1)
iter.sum[7] -= int16(iter.preHash >> 56 & 1)
iter.sum[8] -= int16(iter.preHash >> 55 & 1)
iter.sum[9] -= int16(iter.preHash >> 54 & 1)
iter.sum[10] -= int16(iter.preHash >> 53 & 1)
iter.sum[11] -= int16(iter.preHash >> 52 & 1)
iter.sum[12] -= int16(iter.preHash >> 51 & 1)
iter.sum[13] -= int16(iter.preHash >> 50 & 1)
iter.sum[14] -= int16(iter.preHash >> 49 & 1)
iter.sum[15] -= int16(iter.preHash >> 48 & 1)
iter.sum[16] -= int16(iter.preHash >> 47 & 1)
iter.sum[17] -= int16(iter.preHash >> 46 & 1)
iter.sum[18] -= int16(iter.preHash >> 45 & 1)
iter.sum[19] -= int16(iter.preHash >> 44 & 1)
iter.sum[20] -= int16(iter.preHash >> 43 & 1)
iter.sum[21] -= int16(iter.preHash >> 42 & 1)
iter.sum[22] -= int16(iter.preHash >> 41 & 1)
iter.sum[23] -= int16(iter.preHash >> 40 & 1)
iter.sum[24] -= int16(iter.preHash >> 39 & 1)
iter.sum[25] -= int16(iter.preHash >> 38 & 1)
iter.sum[26] -= int16(iter.preHash >> 37 & 1)
iter.sum[27] -= int16(iter.preHash >> 36 & 1)
iter.sum[28] -= int16(iter.preHash >> 35 & 1)
iter.sum[29] -= int16(iter.preHash >> 34 & 1)
iter.sum[30] -= int16(iter.preHash >> 33 & 1)
iter.sum[31] -= int16(iter.preHash >> 32 & 1)
iter.sum[32] -= int16(iter.preHash >> 31 & 1)
iter.sum[33] -= int16(iter.preHash >> 30 & 1)
iter.sum[34] -= int16(iter.preHash >> 29 & 1)
iter.sum[35] -= int16(iter.preHash >> 28 & 1)
iter.sum[36] -= int16(iter.preHash >> 27 & 1)
iter.sum[37] -= int16(iter.preHash >> 26 & 1)
iter.sum[38] -= int16(iter.preHash >> 25 & 1)
iter.sum[39] -= int16(iter.preHash >> 24 & 1)
iter.sum[40] -= int16(iter.preHash >> 23 & 1)
iter.sum[41] -= int16(iter.preHash >> 22 & 1)
iter.sum[42] -= int16(iter.preHash >> 21 & 1)
iter.sum[43] -= int16(iter.preHash >> 20 & 1)
iter.sum[44] -= int16(iter.preHash >> 19 & 1)
iter.sum[45] -= int16(iter.preHash >> 18 & 1)
iter.sum[46] -= int16(iter.preHash >> 17 & 1)
iter.sum[47] -= int16(iter.preHash >> 16 & 1)
iter.sum[48] -= int16(iter.preHash >> 15 & 1)
iter.sum[49] -= int16(iter.preHash >> 14 & 1)
iter.sum[50] -= int16(iter.preHash >> 13 & 1)
iter.sum[51] -= int16(iter.preHash >> 12 & 1)
iter.sum[52] -= int16(iter.preHash >> 11 & 1)
iter.sum[53] -= int16(iter.preHash >> 10 & 1)
iter.sum[54] -= int16(iter.preHash >> 9 & 1)
iter.sum[55] -= int16(iter.preHash >> 8 & 1)
iter.sum[56] -= int16(iter.preHash >> 7 & 1)
iter.sum[57] -= int16(iter.preHash >> 6 & 1)
iter.sum[58] -= int16(iter.preHash >> 5 & 1)
iter.sum[59] -= int16(iter.preHash >> 4 & 1)
iter.sum[60] -= int16(iter.preHash >> 3 & 1)
iter.sum[61] -= int16(iter.preHash >> 2 & 1)
iter.sum[62] -= int16(iter.preHash >> 1 & 1)
iter.sum[63] -= int16(iter.preHash & 1)
}
// add newly added m-mer
iter._hash, _ = iter.hasher.Next(iter.canonical)
if iter.fracMinHash && iter._hash > iter.maxHash { // discard it, see sourmash paper for FacMinHash
iter._hash = 0
} else if iter._hash > 0 {
iter.nPosHash++
}
// fmt.Printf("[%d] new: %064b\n", iter.idx, iter._hash)
iter.hashes[iter.preHashI] = iter._hash // update the hash value
if iter._hash > 0 {
iter.sum[0] += int16(iter._hash >> 63 & 1)
iter.sum[1] += int16(iter._hash >> 62 & 1)
iter.sum[2] += int16(iter._hash >> 61 & 1)
iter.sum[3] += int16(iter._hash >> 60 & 1)
iter.sum[4] += int16(iter._hash >> 59 & 1)
iter.sum[5] += int16(iter._hash >> 58 & 1)
iter.sum[6] += int16(iter._hash >> 57 & 1)
iter.sum[7] += int16(iter._hash >> 56 & 1)
iter.sum[8] += int16(iter._hash >> 55 & 1)
iter.sum[9] += int16(iter._hash >> 54 & 1)
iter.sum[10] += int16(iter._hash >> 53 & 1)
iter.sum[11] += int16(iter._hash >> 52 & 1)
iter.sum[12] += int16(iter._hash >> 51 & 1)
iter.sum[13] += int16(iter._hash >> 50 & 1)
iter.sum[14] += int16(iter._hash >> 49 & 1)
iter.sum[15] += int16(iter._hash >> 48 & 1)
iter.sum[16] += int16(iter._hash >> 47 & 1)
iter.sum[17] += int16(iter._hash >> 46 & 1)
iter.sum[18] += int16(iter._hash >> 45 & 1)
iter.sum[19] += int16(iter._hash >> 44 & 1)
iter.sum[20] += int16(iter._hash >> 43 & 1)
iter.sum[21] += int16(iter._hash >> 42 & 1)
iter.sum[22] += int16(iter._hash >> 41 & 1)
iter.sum[23] += int16(iter._hash >> 40 & 1)
iter.sum[24] += int16(iter._hash >> 39 & 1)
iter.sum[25] += int16(iter._hash >> 38 & 1)
iter.sum[26] += int16(iter._hash >> 37 & 1)
iter.sum[27] += int16(iter._hash >> 36 & 1)
iter.sum[28] += int16(iter._hash >> 35 & 1)
iter.sum[29] += int16(iter._hash >> 34 & 1)
iter.sum[30] += int16(iter._hash >> 33 & 1)
iter.sum[31] += int16(iter._hash >> 32 & 1)
iter.sum[32] += int16(iter._hash >> 31 & 1)
iter.sum[33] += int16(iter._hash >> 30 & 1)
iter.sum[34] += int16(iter._hash >> 29 & 1)
iter.sum[35] += int16(iter._hash >> 28 & 1)
iter.sum[36] += int16(iter._hash >> 27 & 1)
iter.sum[37] += int16(iter._hash >> 26 & 1)
iter.sum[38] += int16(iter._hash >> 25 & 1)
iter.sum[39] += int16(iter._hash >> 24 & 1)
iter.sum[40] += int16(iter._hash >> 23 & 1)
iter.sum[41] += int16(iter._hash >> 22 & 1)
iter.sum[42] += int16(iter._hash >> 21 & 1)
iter.sum[43] += int16(iter._hash >> 20 & 1)
iter.sum[44] += int16(iter._hash >> 19 & 1)
iter.sum[45] += int16(iter._hash >> 18 & 1)
iter.sum[46] += int16(iter._hash >> 17 & 1)
iter.sum[47] += int16(iter._hash >> 16 & 1)
iter.sum[48] += int16(iter._hash >> 15 & 1)
iter.sum[49] += int16(iter._hash >> 14 & 1)
iter.sum[50] += int16(iter._hash >> 13 & 1)
iter.sum[51] += int16(iter._hash >> 12 & 1)
iter.sum[52] += int16(iter._hash >> 11 & 1)
iter.sum[53] += int16(iter._hash >> 10 & 1)
iter.sum[54] += int16(iter._hash >> 9 & 1)
iter.sum[55] += int16(iter._hash >> 8 & 1)
iter.sum[56] += int16(iter._hash >> 7 & 1)
iter.sum[57] += int16(iter._hash >> 6 & 1)
iter.sum[58] += int16(iter._hash >> 5 & 1)
iter.sum[59] += int16(iter._hash >> 4 & 1)
iter.sum[60] += int16(iter._hash >> 3 & 1)
iter.sum[61] += int16(iter._hash >> 2 & 1)
iter.sum[62] += int16(iter._hash >> 1 & 1)
iter.sum[63] += int16(iter._hash & 1)
}
// decoding vector to hash
code = 0
iter.nThsld = (iter.nPosHash + 1) / 2 // the threshold
// fmt.Printf("nThsld: %d\n", iter.nThsld)
if iter.nPosHash > 0 {
// if n >= N/2 ? 1 : 0
code |= uint64((iter.sum[0]-iter.nThsld)>>15&1^1) << 63
code |= uint64((iter.sum[1]-iter.nThsld)>>15&1^1) << 62
code |= uint64((iter.sum[2]-iter.nThsld)>>15&1^1) << 61
code |= uint64((iter.sum[3]-iter.nThsld)>>15&1^1) << 60
code |= uint64((iter.sum[4]-iter.nThsld)>>15&1^1) << 59
code |= uint64((iter.sum[5]-iter.nThsld)>>15&1^1) << 58
code |= uint64((iter.sum[6]-iter.nThsld)>>15&1^1) << 57
code |= uint64((iter.sum[7]-iter.nThsld)>>15&1^1) << 56
code |= uint64((iter.sum[8]-iter.nThsld)>>15&1^1) << 55
code |= uint64((iter.sum[9]-iter.nThsld)>>15&1^1) << 54
code |= uint64((iter.sum[10]-iter.nThsld)>>15&1^1) << 53
code |= uint64((iter.sum[11]-iter.nThsld)>>15&1^1) << 52
code |= uint64((iter.sum[12]-iter.nThsld)>>15&1^1) << 51
code |= uint64((iter.sum[13]-iter.nThsld)>>15&1^1) << 50
code |= uint64((iter.sum[14]-iter.nThsld)>>15&1^1) << 49
code |= uint64((iter.sum[15]-iter.nThsld)>>15&1^1) << 48
code |= uint64((iter.sum[16]-iter.nThsld)>>15&1^1) << 47
code |= uint64((iter.sum[17]-iter.nThsld)>>15&1^1) << 46
code |= uint64((iter.sum[18]-iter.nThsld)>>15&1^1) << 45
code |= uint64((iter.sum[19]-iter.nThsld)>>15&1^1) << 44
code |= uint64((iter.sum[20]-iter.nThsld)>>15&1^1) << 43
code |= uint64((iter.sum[21]-iter.nThsld)>>15&1^1) << 42
code |= uint64((iter.sum[22]-iter.nThsld)>>15&1^1) << 41
code |= uint64((iter.sum[23]-iter.nThsld)>>15&1^1) << 40
code |= uint64((iter.sum[24]-iter.nThsld)>>15&1^1) << 39
code |= uint64((iter.sum[25]-iter.nThsld)>>15&1^1) << 38
code |= uint64((iter.sum[26]-iter.nThsld)>>15&1^1) << 37
code |= uint64((iter.sum[27]-iter.nThsld)>>15&1^1) << 36
code |= uint64((iter.sum[28]-iter.nThsld)>>15&1^1) << 35
code |= uint64((iter.sum[29]-iter.nThsld)>>15&1^1) << 34
code |= uint64((iter.sum[30]-iter.nThsld)>>15&1^1) << 33
code |= uint64((iter.sum[31]-iter.nThsld)>>15&1^1) << 32
code |= uint64((iter.sum[32]-iter.nThsld)>>15&1^1) << 31
code |= uint64((iter.sum[33]-iter.nThsld)>>15&1^1) << 30
code |= uint64((iter.sum[34]-iter.nThsld)>>15&1^1) << 29
code |= uint64((iter.sum[35]-iter.nThsld)>>15&1^1) << 28
code |= uint64((iter.sum[36]-iter.nThsld)>>15&1^1) << 27
code |= uint64((iter.sum[37]-iter.nThsld)>>15&1^1) << 26
code |= uint64((iter.sum[38]-iter.nThsld)>>15&1^1) << 25
code |= uint64((iter.sum[39]-iter.nThsld)>>15&1^1) << 24
code |= uint64((iter.sum[40]-iter.nThsld)>>15&1^1) << 23
code |= uint64((iter.sum[41]-iter.nThsld)>>15&1^1) << 22
code |= uint64((iter.sum[42]-iter.nThsld)>>15&1^1) << 21
code |= uint64((iter.sum[43]-iter.nThsld)>>15&1^1) << 20
code |= uint64((iter.sum[44]-iter.nThsld)>>15&1^1) << 19
code |= uint64((iter.sum[45]-iter.nThsld)>>15&1^1) << 18
code |= uint64((iter.sum[46]-iter.nThsld)>>15&1^1) << 17
code |= uint64((iter.sum[47]-iter.nThsld)>>15&1^1) << 16
code |= uint64((iter.sum[48]-iter.nThsld)>>15&1^1) << 15
code |= uint64((iter.sum[49]-iter.nThsld)>>15&1^1) << 14
code |= uint64((iter.sum[50]-iter.nThsld)>>15&1^1) << 13
code |= uint64((iter.sum[51]-iter.nThsld)>>15&1^1) << 12
code |= uint64((iter.sum[52]-iter.nThsld)>>15&1^1) << 11
code |= uint64((iter.sum[53]-iter.nThsld)>>15&1^1) << 10
code |= uint64((iter.sum[54]-iter.nThsld)>>15&1^1) << 9
code |= uint64((iter.sum[55]-iter.nThsld)>>15&1^1) << 8
code |= uint64((iter.sum[56]-iter.nThsld)>>15&1^1) << 7
code |= uint64((iter.sum[57]-iter.nThsld)>>15&1^1) << 6
code |= uint64((iter.sum[58]-iter.nThsld)>>15&1^1) << 5
code |= uint64((iter.sum[59]-iter.nThsld)>>15&1^1) << 4
code |= uint64((iter.sum[60]-iter.nThsld)>>15&1^1) << 3
code |= uint64((iter.sum[61]-iter.nThsld)>>15&1^1) << 2
code |= uint64((iter.sum[62]-iter.nThsld)>>15&1^1) << 1
code |= uint64((iter.sum[63]-iter.nThsld)>>15&1 ^ 1)
} else {
code = 0
}
// update the preHashI
if iter.preHashI == iter.k-iter.m {
iter.preHashI = 0
} else {
iter.preHashI++
}
} else {
iter.nPosHash = 0
for iter.idxJ = 0; iter.idxJ <= iter.em; iter.idxJ++ {
iter._hash, _ = iter.hasher.Next(iter.canonical)
// fmt.Println(iter.fracMinHash, iter._hash, iter.maxHash, iter._hash > iter.maxHash)
if iter.fracMinHash && iter._hash > iter.maxHash {
iter.hashes[iter.idxJ] = 0
continue
}
iter.hashes[iter.idxJ] = iter._hash
if iter._hash == 0 {
continue
}
iter.nPosHash++
// fmt.Printf("[%02d] %02d: %064b %d\n", iter.idx, iter.idxJ, iter._hash, iter._hash)
iter.sum[0] += int16(iter._hash >> 63 & 1)
iter.sum[1] += int16(iter._hash >> 62 & 1)
iter.sum[2] += int16(iter._hash >> 61 & 1)
iter.sum[3] += int16(iter._hash >> 60 & 1)
iter.sum[4] += int16(iter._hash >> 59 & 1)
iter.sum[5] += int16(iter._hash >> 58 & 1)
iter.sum[6] += int16(iter._hash >> 57 & 1)
iter.sum[7] += int16(iter._hash >> 56 & 1)
iter.sum[8] += int16(iter._hash >> 55 & 1)
iter.sum[9] += int16(iter._hash >> 54 & 1)
iter.sum[10] += int16(iter._hash >> 53 & 1)
iter.sum[11] += int16(iter._hash >> 52 & 1)
iter.sum[12] += int16(iter._hash >> 51 & 1)
iter.sum[13] += int16(iter._hash >> 50 & 1)
iter.sum[14] += int16(iter._hash >> 49 & 1)
iter.sum[15] += int16(iter._hash >> 48 & 1)
iter.sum[16] += int16(iter._hash >> 47 & 1)
iter.sum[17] += int16(iter._hash >> 46 & 1)
iter.sum[18] += int16(iter._hash >> 45 & 1)
iter.sum[19] += int16(iter._hash >> 44 & 1)
iter.sum[20] += int16(iter._hash >> 43 & 1)
iter.sum[21] += int16(iter._hash >> 42 & 1)
iter.sum[22] += int16(iter._hash >> 41 & 1)
iter.sum[23] += int16(iter._hash >> 40 & 1)
iter.sum[24] += int16(iter._hash >> 39 & 1)
iter.sum[25] += int16(iter._hash >> 38 & 1)
iter.sum[26] += int16(iter._hash >> 37 & 1)
iter.sum[27] += int16(iter._hash >> 36 & 1)
iter.sum[28] += int16(iter._hash >> 35 & 1)
iter.sum[29] += int16(iter._hash >> 34 & 1)
iter.sum[30] += int16(iter._hash >> 33 & 1)
iter.sum[31] += int16(iter._hash >> 32 & 1)
iter.sum[32] += int16(iter._hash >> 31 & 1)
iter.sum[33] += int16(iter._hash >> 30 & 1)
iter.sum[34] += int16(iter._hash >> 29 & 1)
iter.sum[35] += int16(iter._hash >> 28 & 1)
iter.sum[36] += int16(iter._hash >> 27 & 1)
iter.sum[37] += int16(iter._hash >> 26 & 1)
iter.sum[38] += int16(iter._hash >> 25 & 1)
iter.sum[39] += int16(iter._hash >> 24 & 1)
iter.sum[40] += int16(iter._hash >> 23 & 1)
iter.sum[41] += int16(iter._hash >> 22 & 1)
iter.sum[42] += int16(iter._hash >> 21 & 1)
iter.sum[43] += int16(iter._hash >> 20 & 1)
iter.sum[44] += int16(iter._hash >> 19 & 1)
iter.sum[45] += int16(iter._hash >> 18 & 1)
iter.sum[46] += int16(iter._hash >> 17 & 1)
iter.sum[47] += int16(iter._hash >> 16 & 1)
iter.sum[48] += int16(iter._hash >> 15 & 1)
iter.sum[49] += int16(iter._hash >> 14 & 1)
iter.sum[50] += int16(iter._hash >> 13 & 1)
iter.sum[51] += int16(iter._hash >> 12 & 1)
iter.sum[52] += int16(iter._hash >> 11 & 1)
iter.sum[53] += int16(iter._hash >> 10 & 1)
iter.sum[54] += int16(iter._hash >> 9 & 1)
iter.sum[55] += int16(iter._hash >> 8 & 1)
iter.sum[56] += int16(iter._hash >> 7 & 1)
iter.sum[57] += int16(iter._hash >> 6 & 1)
iter.sum[58] += int16(iter._hash >> 5 & 1)
iter.sum[59] += int16(iter._hash >> 4 & 1)
iter.sum[60] += int16(iter._hash >> 3 & 1)
iter.sum[61] += int16(iter._hash >> 2 & 1)
iter.sum[62] += int16(iter._hash >> 1 & 1)
iter.sum[63] += int16(iter._hash & 1)
}
// fmt.Printf(" sum: %v\n", iter.sum)
code = 0
iter.nThsld = (iter.nPosHash + 1) / 2
// fmt.Printf("nThsld: %d\n", iter.nThsld)
if iter.nPosHash > 0 {
// if n >= N/2 ? 1 : 0
code |= uint64((iter.sum[0]-iter.nThsld)>>15&1^1) << 63
code |= uint64((iter.sum[1]-iter.nThsld)>>15&1^1) << 62
code |= uint64((iter.sum[2]-iter.nThsld)>>15&1^1) << 61
code |= uint64((iter.sum[3]-iter.nThsld)>>15&1^1) << 60
code |= uint64((iter.sum[4]-iter.nThsld)>>15&1^1) << 59
code |= uint64((iter.sum[5]-iter.nThsld)>>15&1^1) << 58
code |= uint64((iter.sum[6]-iter.nThsld)>>15&1^1) << 57
code |= uint64((iter.sum[7]-iter.nThsld)>>15&1^1) << 56
code |= uint64((iter.sum[8]-iter.nThsld)>>15&1^1) << 55
code |= uint64((iter.sum[9]-iter.nThsld)>>15&1^1) << 54
code |= uint64((iter.sum[10]-iter.nThsld)>>15&1^1) << 53
code |= uint64((iter.sum[11]-iter.nThsld)>>15&1^1) << 52
code |= uint64((iter.sum[12]-iter.nThsld)>>15&1^1) << 51
code |= uint64((iter.sum[13]-iter.nThsld)>>15&1^1) << 50
code |= uint64((iter.sum[14]-iter.nThsld)>>15&1^1) << 49
code |= uint64((iter.sum[15]-iter.nThsld)>>15&1^1) << 48
code |= uint64((iter.sum[16]-iter.nThsld)>>15&1^1) << 47
code |= uint64((iter.sum[17]-iter.nThsld)>>15&1^1) << 46
code |= uint64((iter.sum[18]-iter.nThsld)>>15&1^1) << 45
code |= uint64((iter.sum[19]-iter.nThsld)>>15&1^1) << 44
code |= uint64((iter.sum[20]-iter.nThsld)>>15&1^1) << 43
code |= uint64((iter.sum[21]-iter.nThsld)>>15&1^1) << 42
code |= uint64((iter.sum[22]-iter.nThsld)>>15&1^1) << 41
code |= uint64((iter.sum[23]-iter.nThsld)>>15&1^1) << 40
code |= uint64((iter.sum[24]-iter.nThsld)>>15&1^1) << 39
code |= uint64((iter.sum[25]-iter.nThsld)>>15&1^1) << 38
code |= uint64((iter.sum[26]-iter.nThsld)>>15&1^1) << 37
code |= uint64((iter.sum[27]-iter.nThsld)>>15&1^1) << 36
code |= uint64((iter.sum[28]-iter.nThsld)>>15&1^1) << 35
code |= uint64((iter.sum[29]-iter.nThsld)>>15&1^1) << 34
code |= uint64((iter.sum[30]-iter.nThsld)>>15&1^1) << 33
code |= uint64((iter.sum[31]-iter.nThsld)>>15&1^1) << 32
code |= uint64((iter.sum[32]-iter.nThsld)>>15&1^1) << 31
code |= uint64((iter.sum[33]-iter.nThsld)>>15&1^1) << 30
code |= uint64((iter.sum[34]-iter.nThsld)>>15&1^1) << 29
code |= uint64((iter.sum[35]-iter.nThsld)>>15&1^1) << 28
code |= uint64((iter.sum[36]-iter.nThsld)>>15&1^1) << 27
code |= uint64((iter.sum[37]-iter.nThsld)>>15&1^1) << 26
code |= uint64((iter.sum[38]-iter.nThsld)>>15&1^1) << 25
code |= uint64((iter.sum[39]-iter.nThsld)>>15&1^1) << 24
code |= uint64((iter.sum[40]-iter.nThsld)>>15&1^1) << 23
code |= uint64((iter.sum[41]-iter.nThsld)>>15&1^1) << 22
code |= uint64((iter.sum[42]-iter.nThsld)>>15&1^1) << 21
code |= uint64((iter.sum[43]-iter.nThsld)>>15&1^1) << 20
code |= uint64((iter.sum[44]-iter.nThsld)>>15&1^1) << 19
code |= uint64((iter.sum[45]-iter.nThsld)>>15&1^1) << 18
code |= uint64((iter.sum[46]-iter.nThsld)>>15&1^1) << 17
code |= uint64((iter.sum[47]-iter.nThsld)>>15&1^1) << 16
code |= uint64((iter.sum[48]-iter.nThsld)>>15&1^1) << 15
code |= uint64((iter.sum[49]-iter.nThsld)>>15&1^1) << 14
code |= uint64((iter.sum[50]-iter.nThsld)>>15&1^1) << 13
code |= uint64((iter.sum[51]-iter.nThsld)>>15&1^1) << 12
code |= uint64((iter.sum[52]-iter.nThsld)>>15&1^1) << 11
code |= uint64((iter.sum[53]-iter.nThsld)>>15&1^1) << 10
code |= uint64((iter.sum[54]-iter.nThsld)>>15&1^1) << 9
code |= uint64((iter.sum[55]-iter.nThsld)>>15&1^1) << 8
code |= uint64((iter.sum[56]-iter.nThsld)>>15&1^1) << 7
code |= uint64((iter.sum[57]-iter.nThsld)>>15&1^1) << 6
code |= uint64((iter.sum[58]-iter.nThsld)>>15&1^1) << 5
code |= uint64((iter.sum[59]-iter.nThsld)>>15&1^1) << 4
code |= uint64((iter.sum[60]-iter.nThsld)>>15&1^1) << 3
code |= uint64((iter.sum[61]-iter.nThsld)>>15&1^1) << 2
code |= uint64((iter.sum[62]-iter.nThsld)>>15&1^1) << 1
code |= uint64((iter.sum[63]-iter.nThsld)>>15&1 ^ 1)
} else {
code = 0
}
iter.preHashI = 0
iter.first = false
}
// code &= 0xffffffff
// fmt.Printf("kmer: %03d-%s, %064b, %d\n\n", iter.idx, iter.s.Seq[iter.idx:iter.idx+iter.k], code, code)
iter.preCode = code
iter.idx++
return code, true
}
// NewHashIterator returns ntHash Iterator.
func NewHashIterator(s *seq.Seq, k int, canonical bool, circular bool) (*Iterator, error) {
if k < 1 {
return nil, ErrInvalidK
}
if len(s.Seq) < k {
return nil, ErrShortSeq
}
// iter := &Iterator{s: s, k: k, canonical: canonical, circular: circular}
iter := poolIterator.Get().(*Iterator)
iter.s = s
iter.k = k
iter.canonical = canonical
iter.circular = circular
iter.finished = false
iter.revcomStrand = false
iter.idx = 0
iter.hash = true
iter.kUint = uint(k)
iter.kP1 = k - 1
iter.kP1Uint = uint(k - 1)
// iter.mask1 = (1 << (iter.kP1Uint << 1)) - 1
// iter.mask2 = iter.kP1Uint << 1
var err error
var seq2 []byte
if circular {
seq2 = make([]byte, len(s.Seq), len(s.Seq)+k-1)
copy(seq2, s.Seq) // do not edit original sequence
seq2 = append(seq2, s.Seq[0:k-1]...)
} else {
seq2 = s.Seq
}
iter.hasher, err = nthash.NewHasher(&seq2, uint(k))
if err != nil {
return nil, err
}
return iter, nil
}
// NextHash returns next ntHash.
func (iter *Iterator) NextHash() (code uint64, ok bool) {
code, ok = iter.hasher.Next(iter.canonical)
if !ok {
poolIterator.Put(iter)
}
iter.idx++
return code, ok
}
// NewKmerIterator returns k-mer code iterator.
func NewKmerIterator(s *seq.Seq, k int, canonical bool, circular bool) (*Iterator, error) {
if k < 1 {
return nil, ErrInvalidK
}
if len(s.Seq) < k {
return nil, ErrShortSeq
}
var s2 *seq.Seq
if circular {
s2 = s.Clone() // do not edit original sequence
s2.Seq = append(s2.Seq, s.Seq[0:k-1]...)
} else {
s2 = s
}
// iter := &Iterator{s: s2, k: k, canonical: canonical, circular: circular}
iter := poolIterator.Get().(*Iterator)
iter.s = s2
iter.k = k
iter.canonical = canonical
iter.circular = circular
iter.finished = false
iter.revcomStrand = false
iter.idx = 0
iter.length = len(s2.Seq)
iter.end = iter.length - k + 1
iter.kUint = uint(k)
iter.kP1 = k - 1
iter.kP1Uint = uint(k - 1)
iter.mask1 = (1 << (iter.kP1Uint << 1)) - 1
iter.mask2 = iter.kP1Uint << 1
iter.first = true
return iter, nil
}
// NextKmer returns next k-mer code.
func (iter *Iterator) NextKmer() (code uint64, ok bool, err error) {
if iter.finished {
return 0, false, nil
}
if iter.idx == iter.end {
if iter.canonical || iter.revcomStrand {
iter.finished = true
poolIterator.Put(iter)
return 0, false, nil
}
iter.s.RevComInplace()
iter.idx = 0
iter.revcomStrand = true
iter.first = true
}
iter.e = iter.idx + iter.k
iter.kmer = iter.s.Seq[iter.idx:iter.e]
if !iter.first {
iter.codeBase = base2bit[iter.kmer[iter.kP1]]
if iter.codeBase == 4 {
err = ErrIllegalBase
}
// compute code from previous one
// code = iter.preCode&((1<<(iter.kP1Uint<<1))-1)<<2 | iter.codeBase
code = (iter.preCode&iter.mask1)<<2 | iter.codeBase
// compute code of revcomp kmer from previous one
// iter.codeRC = (iter.codeBase^3)<<(iter.kP1Uint<<1) | (iter.preCodeRC >> 2)
iter.codeRC = (iter.codeBase^3)<<(iter.mask2) | (iter.preCodeRC >> 2)
} else {
code, err = kmers.Encode(iter.kmer)
iter.codeRC = kmers.MustRevComp(code, iter.k)
iter.first = false
}
if err != nil {
return 0, false, fmt.Errorf("encode %s: %s", iter.kmer, err)
}
iter.preCode = code
iter.preCodeRC = iter.codeRC
iter.idx++
if iter.canonical && code > iter.codeRC {
code = iter.codeRC
}
return code, true, nil
}
// Next is a wrapter for NextHash and NextKmer.
func (iter *Iterator) Next() (code uint64, ok bool, err error) {
if iter.hash {
if iter.simhash {
code, ok = iter.NextSimHash()
return
}
code, ok = iter.NextHash()
return
}
code, ok, err = iter.NextKmer()
return
}
// Index returns current 0-baesd index.
func (iter *Iterator) Index() int {
return iter.idx - 1
}
bio-0.13.3/sketches/iterator_test.go 0000664 0000000 0000000 00000014736 14573550650 0017424 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
import (
"math/rand"
"testing"
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/util/bytesize"
)
func TestKmerIterator(t *testing.T) {
_s := "AAGTTTGAATCATTCAACTATCTAGTTTTCAGAGAACAATGTTCTCTAAAGAATAGAAAAGAGTCATTGTGCGGTGATGATGGCGGGAAGGATCCACCTG"
sequence, err := seq.NewSeq(seq.DNA, []byte(_s))
if err != nil {
t.Errorf("fail to create sequence: %s", _s)
}
k := 10
iter, err := NewKmerIterator(sequence, k, true, false)
if err != nil {
t.Errorf("fail to create aa iter rator")
}
var code uint64
var ok bool
// var idx int
codes := make([]uint64, 0, 1024)
for {
code, ok, err = iter.Next()
if err != nil {
t.Error(err)
}
if !ok {
break
}
// idx = iter.Index()
// fmt.Printf("kmer: %d-%s, %d\n", idx, iter.s.Seq[idx:idx+k], code)
codes = append(codes, code)
}
if len(codes) != len(_s)-k+1 {
t.Errorf("k-mers number error")
}
}
func TestHashIterator(t *testing.T) {
_s := "AAGTTTGAATCATTCAACTATCTAGTTTTCAGAGAACAATGTTCTCTAAAGAATAGAAAAGAGTCATTGTGCGGTGATGATGGCGGGAAGGATCCACCTG"
sequence, err := seq.NewSeq(seq.DNA, []byte(_s))
if err != nil {
t.Errorf("fail to create sequence: %s", _s)
}
k := 10
iter, err := NewHashIterator(sequence, k, true, false)
if err != nil {
t.Errorf("fail to create aa iter rator")
}
var code uint64
var ok bool
// var idx int
codes := make([]uint64, 0, 1024)
for {
code, ok, err = iter.Next()
if err != nil {
t.Error(err)
}
if !ok {
break
}
// idx = iter.Index()
// fmt.Printf("kmer: %d-%s, %d\n", idx, iter.s.Seq[idx:idx+k], code)
codes = append(codes, code)
}
if len(codes) != len(_s)-k+1 {
t.Errorf("k-mer hashes number error")
}
}
func TestSimHashIterator(t *testing.T) {
// _s := "AAGTTTGAATCATTCAACTATCTAGTTTTCAGAGAACAATGTTCTCTAAAGAATAGAAAAGAGTCATTGTGCGGTGATGATGGCGGGAAGGATCCACCTG"
_ss := []string{
// "AAGTTTGAATCATTCAACTATCTAGTTTTCAGAGAACAATGTTCTCTAAAGAATAGAAAAGAGTCATTGTGCGGTGATGATGGCGGGAAGGATCCACCTG",
"GAACAATGTTCTCTAAAATTG",
"GcACAATGTTCTCTAAAATTG",
}
for _, _s := range _ss {
sequence, err := seq.NewSeq(seq.DNA, []byte(_s))
if err != nil {
t.Errorf("fail to create sequence: %s", _s)
}
k := 21
iter, err := NewSimHashIterator(sequence, k, 5, 5, true, false)
if err != nil {
t.Errorf("fail to create aa iter rator")
}
var code uint64
var ok bool
// var idx int
codes := make([]uint64, 0, 1024)
for {
code, ok = iter.NextSimHash()
if !ok {
break
}
// idx = iter.Index()
// fmt.Printf("kmer: %03d-%s, %064b, %d\n", idx, iter.s.Seq[idx:idx+k], code, code)
codes = append(codes, code)
}
if len(codes) != len(_s)-k+1 {
t.Errorf("k-mer hashes number error")
}
}
}
var benchSeqs []*seq.Seq
var _code uint64
func init() {
rand.Seed(11)
sizes := []int{1 << 10} //, 1 << 20, 10 << 20}
benchSeqs = make([]*seq.Seq, len(sizes))
var err error
for i, size := range sizes {
sequence := make([]byte, size)
// fmt.Printf("generating pseudo DNA with length of %s ...\n", bytesize.ByteSize(size))
for j := 0; j < size; j++ {
sequence[j] = bit2base[rand.Intn(4)]
}
benchSeqs[i], err = seq.NewSeq(seq.DNA, sequence)
if err != nil {
panic("should not happen")
}
// fmt.Println(benchSeqs[i])
}
// fmt.Printf("%d DNA sequences generated\n", len(sizes))
}
func BenchmarkKmerIterator(b *testing.B) {
for i := range benchSeqs {
size := len(benchSeqs[i].Seq)
b.Run(bytesize.ByteSize(size).String(), func(b *testing.B) {
var code uint64
var ok bool
for j := 0; j < b.N; j++ {
iter, err := NewKmerIterator(benchSeqs[i], 31, true, false)
if err != nil {
b.Errorf("fail to create hash iterator. seq length: %d", size)
}
for {
code, ok, err = iter.NextKmer()
if err != nil {
b.Errorf("fail to get kmer code: %d-%s", iter.Index(),
benchSeqs[i].Seq[iter.Index():iter.Index()+31])
}
if !ok {
break
}
_code = code
}
}
})
}
}
func BenchmarkHashIterator(b *testing.B) {
for i := range benchSeqs {
size := len(benchSeqs[i].Seq)
b.Run(bytesize.ByteSize(size).String(), func(b *testing.B) {
var code uint64
var ok bool
for j := 0; j < b.N; j++ {
iter, err := NewHashIterator(benchSeqs[i], 31, true, false)
if err != nil {
b.Errorf("fail to create hash iterator. seq length: %d", size)
}
for {
code, ok = iter.NextHash()
if !ok {
break
}
_code = code
}
}
})
}
}
func BenchmarkSimHashIterator(b *testing.B) {
for i := range benchSeqs {
size := len(benchSeqs[i].Seq)
b.Run(bytesize.ByteSize(size).String(), func(b *testing.B) {
var code uint64
var ok bool
for j := 0; j < b.N; j++ {
iter, err := NewSimHashIterator(benchSeqs[i], 31, 5, 5, true, false)
if err != nil {
b.Errorf("fail to create hash iterator. seq length: %d", size)
}
for {
code, ok = iter.NextSimHash()
if !ok {
break
}
_code = code
}
}
})
}
}
func BenchmarkProteinIterator(b *testing.B) {
for i := range benchSeqs {
size := len(benchSeqs[i].Seq)
b.Run(bytesize.ByteSize(size).String(), func(b *testing.B) {
var code uint64
var ok bool
for j := 0; j < b.N; j++ {
iter, err := NewProteinIterator(benchSeqs[i], 10, 1, 1)
if err != nil {
b.Errorf("fail to create hash iterator. seq length: %d", size)
}
for {
code, ok = iter.Next()
if !ok {
break
}
_code = code
}
}
})
}
}
bio-0.13.3/sketches/kmers.go 0000664 0000000 0000000 00000003732 14573550650 0015647 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
var base2bit = [256]uint64{
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 1, 1, 0, 4, 4, 2, 0, 4, 4, 2, 4, 0, 0, 4,
4, 4, 0, 1, 3, 3, 0, 0, 4, 1, 4, 4, 4, 4, 4, 4,
4, 0, 1, 1, 0, 4, 4, 2, 0, 4, 4, 2, 4, 0, 0, 4,
4, 4, 0, 1, 3, 3, 0, 0, 4, 1, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
}
var bit2base = [4]byte{'A', 'C', 'G', 'T'}
bio-0.13.3/sketches/sketch-protein.go 0000664 0000000 0000000 00000011277 14573550650 0017470 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
import (
"sync"
"github.com/shenwei356/bio/seq"
"github.com/twotwotwo/sorts"
"github.com/zeebo/wyhash"
)
// ProteinMinimizerSketch is a protein k-mer minimizer iterator
type ProteinMinimizerSketch struct {
s *seq.Seq // amino acid
k int
end0 int
idx int
// ----------------------
skip bool
w int
end int
r int // L-s
i, mI int
mV uint64
preMinIdx int
buf []IdxValue
i2v IdxValue
flag bool
t, b, e int
}
var poolProteinMinimizerSketch = &sync.Pool{New: func() interface{} {
return &ProteinMinimizerSketch{}
}}
// NewProteinMinimizerSketch returns a ProteinMinimizerSketch
func NewProteinMinimizerSketch(S *seq.Seq, k int, codonTable int, frame int, w int) (*ProteinMinimizerSketch, error) {
if k < 1 {
return nil, ErrInvalidK
}
if len(S.Seq) < k*3 {
return nil, ErrShortSeq
}
if w < 1 || w > (1<<31)-1 {
return nil, ErrInvalidW
}
if len(S.Seq) < k*3+w-1 {
return nil, ErrShortSeq
}
// s := &ProteinMinimizerSketch{s0: S, k: k, w: w}
s := poolProteinMinimizerSketch.Get().(*ProteinMinimizerSketch)
s.k = k
s.w = w
var err error
if S.Alphabet != seq.Protein {
s.s, err = S.Translate(codonTable, frame, false, false, true, false)
if err != nil {
return nil, err
}
} else {
s.s = S
}
s.idx = 0
s.end0 = len(s.s.Seq) - k
s.skip = w == 1
s.end = len(s.s.Seq) - 1
s.r = w - 1 // L-k
s.buf = make([]IdxValue, 0, w)
s.preMinIdx = -1
return s, nil
}
// Next returns next hash value
func (s *ProteinMinimizerSketch) Next() (code uint64, ok bool) {
for {
// if s.idx > s.end {
// return 0, false
// }
if s.idx > s.end0 {
poolProteinIterator.Put(s)
return 0, false
}
code = wyhash.Hash(s.s.Seq[s.idx:s.idx+s.k], 1)
if s.skip {
s.mI = s.idx
s.idx++
return code, true
}
// in window
if s.idx < s.r {
s.buf = append(s.buf, IdxValue{Idx: s.idx, Val: code})
s.idx++
continue
}
// end of w
if s.idx == s.r {
s.buf = append(s.buf, IdxValue{Idx: s.idx, Val: code})
// sort.Sort(idxValues(s.buf)) // sort
sorts.Quicksort(idxValues(s.buf)) // sort
s.i2v = s.buf[0]
s.mI, s.mV = s.i2v.Idx, s.i2v.Val
s.preMinIdx = s.mI
s.idx++
return s.i2v.Val, true
}
// find min k-mer
// remove k-mer not in this window.
// have to check position/index one by one
for s.i, s.i2v = range s.buf {
if s.i2v.Idx == s.idx-s.w {
if s.i < s.r {
copy(s.buf[s.i:s.r], s.buf[s.i+1:])
} // happen to be at the end
s.buf = s.buf[:s.r]
break
}
}
// add new k-mer
s.flag = false
// using binary search, faster han linear search
s.b, s.e = 0, s.r-1
for {
s.t = s.b + (s.e-s.b)/2
if code < s.buf[s.t].Val {
s.e = s.t - 1 // end search here
if s.e <= s.b {
s.flag = true
s.i = s.b
break
}
} else {
s.b = s.t + 1 // start here
if s.b >= s.r {
s.flag = false
break
}
if s.b >= s.e {
s.flag = true
s.i = s.e // right here
break
}
}
}
if !s.flag { // it's the biggest one, append to the end
s.buf = append(s.buf, IdxValue{s.idx, code})
} else {
if code >= s.buf[s.i].Val { // have to check again
s.i++
}
s.buf = append(s.buf, blankI2V) // append one element
copy(s.buf[s.i+1:], s.buf[s.i:s.r]) // move right
s.buf[s.i] = IdxValue{s.idx, code}
}
s.i2v = s.buf[0]
if s.i2v.Idx == s.preMinIdx { // deduplicate
s.idx++
continue
}
s.mI, s.mV = s.i2v.Idx, s.i2v.Val
s.preMinIdx = s.mI
s.idx++
return s.i2v.Val, true
}
}
// Index returns current 0-baesd index.
func (s *ProteinMinimizerSketch) Index() int {
return s.mI
}
bio-0.13.3/sketches/sketch-protein_test.go 0000664 0000000 0000000 00000003552 14573550650 0020524 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
import (
"testing"
"github.com/shenwei356/bio/seq"
)
func TestProteinMinimizer(t *testing.T) {
_s := "AAGTTTGAATCATTCAACTATCTAGTTTTCAGAGAACAATGTTCTCTAAAGAATAGAAAAGAGTCATTGTGCGGTGATGATGGCGGGAAGGATCCACCTG"
sequence, err := seq.NewSeq(seq.DNA, []byte(_s))
if err != nil {
t.Errorf("fail to create sequence: %s", _s)
}
k := 10
w := 3
sketch, err := NewProteinMinimizerSketch(sequence, k, 1, 1, w)
if err != nil {
t.Errorf("fail to create minizimer sketch")
}
var code uint64
var ok bool
// var idx int
codes := make([]uint64, 0, 1024)
for {
code, ok = sketch.Next()
if !ok {
break
}
// idx = sketch.Index()
// fmt.Printf("aa: %d-%s, %d\n", idx, sketch.s.Seq[idx:idx+k], code)
codes = append(codes, code)
}
}
bio-0.13.3/sketches/sketch.go 0000664 0000000 0000000 00000027164 14573550650 0016014 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
import (
"fmt"
"sync"
"github.com/shenwei356/bio/seq"
"github.com/twotwotwo/sorts"
"github.com/will-rowe/nthash"
)
// ErrInvalidS means s >= k.
var ErrInvalidS = fmt.Errorf("kmers: invalid s-mer size")
// ErrInvalidW means w < 2 or w > (1<<32)-1
var ErrInvalidW = fmt.Errorf("kmers: invalid minimimzer window")
// ErrBufNil means the buffer is nil
var ErrBufNil = fmt.Errorf("kmers: buffer slice is nil")
// ErrBufNotEmpty means the buffer has some elements
var ErrBufNotEmpty = fmt.Errorf("kmers: buffer has elements")
// Sketch is a k-mer sketch iterator
type Sketch struct {
S []byte
k int
s int
circular bool
hasher *nthash.NTHi
kMs int // k-s, just for syncmer
r int // L-s
idx int // current location, 0-based
end int
i, mI int
v, mV uint64
preMinIdx int
buf []IdxValue
i2v IdxValue
flag bool
t, b, e int
// ------ just for syncmer -------
hasherS *nthash.NTHi
bsyncmerIdx int
lateOutputThisOne bool
preMinIdxs []int
// ------ just for minimizer -----
skip bool
minimizer bool
w int
}
var poolSketch = &sync.Pool{New: func() interface{} {
return &Sketch{}
}}
// NewMinimizerSketch returns a SyncmerSketch Iterator.
// It returns the minHashes in all windows of w (w>=1) bp.
func NewMinimizerSketch(S *seq.Seq, k int, w int, circular bool) (*Sketch, error) {
if k < 1 {
return nil, ErrInvalidK
}
if w < 1 || w > (1<<31)-1 {
return nil, ErrInvalidW
}
if len(S.Seq) < k+w-1 {
return nil, ErrShortSeq
}
// sketch := &Sketch{S: S.Seq, w: w, k: k, circular: circular}
sketch := poolSketch.Get().(*Sketch)
sketch.minimizer = true
sketch.k = k
sketch.w = w
sketch.circular = circular
sketch.skip = w == 1
var seq2 []byte
if circular {
seq2 = make([]byte, len(S.Seq), len(S.Seq)+k-1)
copy(seq2, S.Seq) // do not edit original sequence
seq2 = append(seq2, S.Seq[0:k-1]...)
sketch.S = seq2
} else {
seq2 = S.Seq
}
sketch.idx = 0
sketch.end = len(seq2) - 1
sketch.r = w - 1 // L-k
var err error
sketch.hasher, err = nthash.NewHasher(&seq2, uint(k))
if err != nil {
return nil, err
}
if sketch.buf == nil {
sketch.buf = make([]IdxValue, 0, w)
} else {
sketch.buf = sketch.buf[:0]
}
if sketch.preMinIdxs == nil {
sketch.preMinIdxs = make([]int, 0, 8)
} else {
sketch.preMinIdxs = sketch.preMinIdxs[:0]
}
sketch.preMinIdx = -1
return sketch, nil
}
// NewSyncmerSketch returns a SyncmerSketch Iterator.
// 1<=s<=k.
func NewSyncmerSketch(S *seq.Seq, k int, s int, circular bool) (*Sketch, error) {
if k < 1 {
return nil, ErrInvalidK
}
if s > k || s == 0 {
return nil, ErrInvalidS
}
if len(S.Seq) < k*2-s-1 {
return nil, ErrShortSeq
}
// sketch := &Sketch{S: S.Seq, s: s, k: k, circular: circular}
sketch := poolSketch.Get().(*Sketch)
sketch.minimizer = false
sketch.k = k
sketch.s = s
sketch.circular = circular
sketch.skip = s == k
var seq2 []byte
if circular {
seq2 = make([]byte, len(S.Seq), len(S.Seq)+k-1)
copy(seq2, S.Seq) // do not edit original sequence
seq2 = append(seq2, S.Seq[0:k-1]...)
sketch.S = seq2
} else {
seq2 = S.Seq
}
sketch.idx = 0
sketch.end = len(seq2) - 2*k + s + 1 // len(sequence) - L (2*k - s - 1)
sketch.r = 2*k - s - 1 - s // L-s
sketch.kMs = k - s // k-s
sketch.w = k - s
var err error
sketch.hasher, err = nthash.NewHasher(&seq2, uint(k))
if err != nil {
return nil, err
}
sketch.hasherS, err = nthash.NewHasher(&seq2, uint(s))
if err != nil {
return nil, err
}
if sketch.buf == nil {
sketch.buf = make([]IdxValue, 0, (k-s)<<1)
} else {
sketch.buf = sketch.buf[:0]
}
if sketch.preMinIdxs == nil {
sketch.preMinIdxs = make([]int, 0, 8)
} else {
sketch.preMinIdxs = sketch.preMinIdxs[:0]
}
sketch.preMinIdx = -1
return sketch, nil
}
// NextMinimizer returns next minimizer.
func (s *Sketch) NextMinimizer() (code uint64, ok bool) {
for {
if s.idx > s.end {
return 0, false
}
// nthash of current k-mer
code, ok = s.hasher.Next(true)
if !ok {
poolSketch.Put(s)
return code, false
}
if s.skip {
s.mI = s.idx
s.idx++
return code, true
}
// in window
if s.idx < s.r {
s.buf = append(s.buf, IdxValue{Idx: s.idx, Val: code})
s.idx++
continue
}
// end of w
if s.idx == s.r {
s.buf = append(s.buf, IdxValue{Idx: s.idx, Val: code})
// sort.Sort(idxValues(s.buf)) // sort
sorts.Quicksort(idxValues(s.buf)) // sort
s.i2v = s.buf[0]
s.mI, s.mV = s.i2v.Idx, s.i2v.Val
s.preMinIdx = s.mI
s.idx++
return s.i2v.Val, true
}
// find min k-mer
// remove k-mer not in this window.
// have to check position/index one by one
for s.i, s.i2v = range s.buf {
if s.i2v.Idx == s.idx-s.w {
if s.i < s.r {
copy(s.buf[s.i:s.r], s.buf[s.i+1:])
} // happen to be at the end
s.buf = s.buf[:s.r]
break
}
}
// add new k-mer
s.flag = false
// using binary search, faster han linear search
s.b, s.e = 0, s.r-1
for {
s.t = s.b + (s.e-s.b)/2
if code < s.buf[s.t].Val {
s.e = s.t - 1 // end search here
if s.e <= s.b {
s.flag = true
s.i = s.b
break
}
} else {
s.b = s.t + 1 // start here
if s.b >= s.r {
s.flag = false
break
}
if s.b >= s.e {
s.flag = true
s.i = s.e // right here
break
}
}
}
if !s.flag { // it's the biggest one, append to the end
s.buf = append(s.buf, IdxValue{s.idx, code})
} else {
if code >= s.buf[s.i].Val { // have to check again
s.i++
}
s.buf = append(s.buf, blankI2V) // append one element
copy(s.buf[s.i+1:], s.buf[s.i:s.r]) // move right
s.buf[s.i] = IdxValue{s.idx, code}
}
s.i2v = s.buf[0]
if s.i2v.Idx == s.preMinIdx { // deduplicate
s.idx++
continue
}
s.mI, s.mV = s.i2v.Idx, s.i2v.Val
s.preMinIdx = s.mI
s.idx++
return s.i2v.Val, true
}
}
// NextSyncmer returns next syncmer.
func (s *Sketch) NextSyncmer() (code uint64, ok bool) {
for {
if s.idx > s.end {
return 0, false
}
// nthash of current k-mer
code, ok = s.hasher.Next(true)
if !ok {
poolSketch.Put(s)
return code, false
}
// fmt.Printf("\nidx: %d, %s, %d\n", s.idx, s.S[s.idx:s.idx+s.s], code)
// fmt.Printf("idx: %d, pres: %v, pre: %d\n", s.idx, s.preMinIdxs, s.preMinIdx)
if s.skip {
s.idx++
return code, true
}
if len(s.preMinIdxs) > 0 && s.idx == s.preMinIdxs[0] {
// we will output this one in this round
s.lateOutputThisOne = true
} else {
s.lateOutputThisOne = false
}
// find min s-mer
if s.idx == 0 {
for s.i = s.idx; s.i <= s.idx+s.r; s.i++ {
// fmt.Printf("s: %d\n", s.i)
s.v, ok = s.hasherS.Next(true)
if !ok {
return code, false
}
s.buf = append(s.buf, IdxValue{Idx: s.i, Val: s.v})
}
// sort.Sort(idxValues(s.buf))
sorts.Quicksort(idxValues(s.buf)) // sort
} else {
// remove s-mer not in this window.
// have to check position/index one by one
for s.i, s.i2v = range s.buf {
if s.i2v.Idx == s.idx-1 {
if s.i < s.r {
copy(s.buf[s.i:s.r], s.buf[s.i+1:])
} // happen to be at the end
s.buf = s.buf[:s.r]
break
}
}
// add new s-mer
// fmt.Printf("s: %d\n", s.idx+s.r)
s.v, ok = s.hasherS.Next(true)
if !ok {
return code, false
}
s.flag = false
// using binary search, faster han linear search
s.b, s.e = 0, s.r-1
for {
s.t = s.b + (s.e-s.b)/2
if s.v < s.buf[s.t].Val {
s.e = s.t - 1 // end search here
if s.e <= s.b {
s.flag = true
s.i = s.b
break
}
} else {
s.b = s.t + 1 // start here
if s.b >= s.r {
s.flag = false
break
}
if s.b >= s.e {
s.flag = true
s.i = s.e // right here
break
}
}
}
if !s.flag { // it's the biggest one, append to the end
s.buf = append(s.buf, IdxValue{s.idx + s.r, s.v})
} else {
if s.v >= s.buf[s.i].Val { // have to check again
s.i++
}
s.buf = append(s.buf, blankI2V) // append one element
copy(s.buf[s.i+1:], s.buf[s.i:s.r]) // move right
s.buf[s.i] = IdxValue{s.idx + s.r, s.v}
}
}
s.i2v = s.buf[0]
s.mI, s.mV = s.i2v.Idx, s.i2v.Val
// fmt.Printf(" smer: %d: %d\n", s.mI, s.mV)
// find the location of bounded syncmer
if s.mI-s.idx < s.w { // syncmer at the beginning of kmer
s.bsyncmerIdx = s.mI
// fmt.Printf(" bIdx: start: %d\n", s.bsyncmerIdx)
} else { // at the end
s.bsyncmerIdx = s.mI - s.kMs
// fmt.Printf(" bIdx: end: %d\n", s.bsyncmerIdx)
}
// ----------------------------------
// duplicated
if len(s.preMinIdxs) > 0 && s.bsyncmerIdx == s.preMinIdxs[0] {
// fmt.Printf(" duplicated: %d\n", s.bsyncmerIdx)
if s.lateOutputThisOne {
// remove the first element
copy(s.preMinIdxs[0:len(s.preMinIdxs)-1], s.preMinIdxs[1:])
s.preMinIdxs = s.preMinIdxs[0 : len(s.preMinIdxs)-1]
s.idx++
s.preMinIdx = s.bsyncmerIdx
return code, true
}
s.idx++
// s.preMinIdx = s.bsyncmerIdx
continue
}
if s.lateOutputThisOne {
// remove the first element
copy(s.preMinIdxs[0:len(s.preMinIdxs)-1], s.preMinIdxs[1:])
s.preMinIdxs = s.preMinIdxs[0 : len(s.preMinIdxs)-1]
if s.preMinIdx != s.bsyncmerIdx {
s.preMinIdxs = append(s.preMinIdxs, s.bsyncmerIdx)
}
// fmt.Printf(" late2: %d\n", s.preMinIdxs[0])
s.idx++
s.preMinIdx = s.bsyncmerIdx
return code, true
}
// is it current kmer?
if s.bsyncmerIdx == s.idx {
// fmt.Printf(" current: %d\n", s.bsyncmerIdx)
if len(s.preMinIdxs) > 0 {
// remove the first element
copy(s.preMinIdxs[0:len(s.preMinIdxs)-1], s.preMinIdxs[1:])
s.preMinIdxs = s.preMinIdxs[0 : len(s.preMinIdxs)-1]
}
s.idx++
s.preMinIdx = s.bsyncmerIdx
return code, true
}
if s.preMinIdx != s.bsyncmerIdx {
s.preMinIdxs = append(s.preMinIdxs, s.bsyncmerIdx)
}
// fmt.Printf(" return it later: %d\n", s.bsyncmerIdx)
s.idx++
s.preMinIdx = s.bsyncmerIdx
}
}
// Next returns next sketch
func (s *Sketch) Next() (uint64, bool) {
if s.minimizer {
return s.NextMinimizer()
}
return s.NextSyncmer()
}
// Index returns current 0-baesd index
func (s *Sketch) Index() int {
if s.minimizer {
return s.mI
}
return s.idx - 1
}
// IdxValue is for storing k-mer hash and it's location when computing k-mer sketches.
type IdxValue struct {
Idx int // index
Val uint64 // hash
}
var blankI2V = IdxValue{0, 0}
type idxValues []IdxValue
func (l idxValues) Len() int { return len(l) }
func (l idxValues) Less(i int, j int) bool { return l[i].Val < l[j].Val }
func (l idxValues) Swap(i int, j int) { l[i], l[j] = l[j], l[i] }
bio-0.13.3/sketches/sketch_test.go 0000664 0000000 0000000 00000012354 14573550650 0017046 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package sketches
import (
"testing"
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/util/bytesize"
)
var _syncmer uint64
var _syncmerIdx int
func TestMinimizer(t *testing.T) {
_s := "GGCAAGTTCGTCA"
// _s := "GGCAAGTTC"
sequence, err := seq.NewSeq(seq.DNA, []byte(_s))
if err != nil {
t.Errorf("fail to create sequence: %s", _s)
}
k := 5
w := 3
sketch, err := NewMinimizerSketch(sequence, k, w, false)
if err != nil {
t.Errorf("fail to create minizimer sketch")
}
var code uint64
var ok bool
var idx int
codes := make([]uint64, 0, 1024)
for {
code, ok = sketch.NextMinimizer()
if !ok {
break
}
idx = sketch.Index()
_syncmerIdx = idx
_syncmer = code
codes = append(codes, code)
// fmt.Printf("minizimer: %d-%s, %d\n", idx, _s[idx:idx+k], code)
}
if len(codes) == 5 &&
codes[0] == 973456138564179607 &&
codes[1] == 2645801399420473919 &&
codes[2] == 1099502864234245338 &&
codes[3] == 6763474888237448943 &&
codes[4] == 2737971715116251183 {
} else {
t.Errorf("minizimer error")
}
}
func TestSyncmer(t *testing.T) {
_s := "GGCAAGTTCGTCATCGATC"
// _s := "GGCAAGTTC"
sequence, err := seq.NewSeq(seq.DNA, []byte(_s))
if err != nil {
t.Errorf("fail to create sequence: %s", _s)
}
k := 5
s := 2
sketch, err := NewSyncmerSketch(sequence, k, s, false)
if err != nil {
t.Errorf("fail to create syncmer sketch")
}
var code uint64
var ok bool
var idx int
codes := make([]uint64, 0, 1024)
for {
code, ok = sketch.NextSyncmer()
// fmt.Println(sketch.Index(), code, ok)
if !ok {
break
}
idx = sketch.Index()
_syncmerIdx = idx
_syncmer = code
codes = append(codes, code)
// fmt.Printf("syncmer: %d-%s, %d\n", idx, _s[idx:idx+k], code)
}
// if len(codes) == 5 &&
// codes[0] == 7385093395039290540 &&
// codes[1] == 1099502864234245338 {
// } else {
// t.Errorf("syncmer error")
// }
}
func BenchmarkMinimizerSketch(b *testing.B) {
for i := range benchSeqs {
size := len(benchSeqs[i].Seq)
b.Run(bytesize.ByteSize(size).String(), func(b *testing.B) {
var code uint64
var ok bool
// var n int
for j := 0; j < b.N; j++ {
iter, err := NewMinimizerSketch(benchSeqs[i], 31, 15, false)
if err != nil {
b.Errorf("fail to create minizimer sketch. seq length: %d", size)
}
// n = 0
for {
code, ok = iter.NextMinimizer()
if !ok {
break
}
// fmt.Printf("minizimer: %d-%d\n", iter.Index(), code)
_code = code
// n++
}
}
// fmt.Printf("minizimer for %s DNA, c=%.6f\n", bytesize.ByteSize(size).String(), float64(size)/float64(n))
})
}
}
// go test -v -test.bench=BenchmarkSyncmerSketch -cpuprofile profile.out -test.run=damnit
// go tool pprof -http=:8080 profile.out
func BenchmarkSyncmerSketch(b *testing.B) {
for i := range benchSeqs {
size := len(benchSeqs[i].Seq)
b.Run(bytesize.ByteSize(size).String(), func(b *testing.B) {
var code uint64
var ok bool
// var n int
for j := 0; j < b.N; j++ {
iter, err := NewSyncmerSketch(benchSeqs[i], 31, 16, false)
if err != nil {
b.Errorf("fail to create syncmer sketch. seq length: %d", size)
}
// n = 0
for {
code, ok = iter.NextSyncmer()
if !ok {
break
}
// fmt.Printf("syncmer: %d-%d\n", iter.Index(), code)
_code = code
// n++
}
}
// fmt.Printf("syncmer for %s DNA, c=%.6f\n", bytesize.ByteSize(size).String(), float64(size)/float64(n))
})
}
}
func BenchmarkProteinMinimizerSketch(b *testing.B) {
for i := range benchSeqs {
size := len(benchSeqs[i].Seq)
b.Run(bytesize.ByteSize(size).String(), func(b *testing.B) {
var code uint64
var ok bool
// var n int
for j := 0; j < b.N; j++ {
iter, err := NewProteinMinimizerSketch(benchSeqs[i], 10, 1, 1, 5)
if err != nil {
b.Errorf("fail to create minizimer sketch. seq length: %d", size)
}
// n = 0
for {
code, ok = iter.Next()
if !ok {
break
}
// fmt.Printf("minizimer: %d-%d\n", iter.Index(), code)
_code = code
// n++
}
}
// fmt.Printf("minizimer for %s Protein, c=%.6f\n", bytesize.ByteSize(size).String(), float64(size)/float64(n))
})
}
}
bio-0.13.3/taxdump/ 0000775 0000000 0000000 00000000000 14573550650 0014043 5 ustar 00root root 0000000 0000000 bio-0.13.3/taxdump/README.md 0000775 0000000 0000000 00000000514 14573550650 0015325 0 ustar 00root root 0000000 0000000 # taxdump
[](https://pkg.go.dev/github.com/shenwei356/bio/taxdump)
This package provides querying manipulations from NCBI Taxonomy taxdump files.
## History
This package was originally maintained in [unikmer](https://github.com/shenwei356/unikmer).
bio-0.13.3/taxdump/taxonomy.go 0000664 0000000 0000000 00000037373 14573550650 0016265 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package taxdump
import (
"bufio"
"errors"
"fmt"
"strconv"
"strings"
"sync"
"github.com/shenwei356/xopen"
)
// Taxonomy holds relationship of taxon in a taxonomy.
type Taxonomy struct {
file string
rootNode uint32
Nodes map[uint32]uint32 // child -> parent
DelNodes map[uint32]struct{}
MergeNodes map[uint32]uint32 // from -> to
Names map[uint32]string
taxid2rankid map[uint32]uint8 // taxid -> rank id
ranks []string // rank id -> rank
Ranks map[string]interface{}
hasRanks bool
hasDelNodes bool
hasMergeNodes bool
hasNames bool
cacheLCA bool
lcaCache sync.Map
maxTaxid uint32
}
// ErrIllegalColumnIndex means column index is 0 or negative.
var ErrIllegalColumnIndex = errors.New("taxdump: illegal column index, positive integer needed")
// ErrRankNotLoaded means you should reate load Taxonomy with NewTaxonomyWithRank before calling some methods.
var ErrRankNotLoaded = errors.New("taxdump: taxonomic ranks not loaded, please call: NewTaxonomyWithRank")
// ErrNamesNotLoaded means you should call LoadNames before using taxonomy names.
var ErrNamesNotLoaded = errors.New("taxdump: taxonomy names not loaded, please call: LoadNames")
// ErrTooManyRanks means number of ranks exceed limit of 255
var ErrTooManyRanks = errors.New("taxdump: number of ranks exceed limit of 255")
// ErrUnkownRank indicate an unknown rank
var ErrUnkownRank = errors.New("taxdump: unknown rank")
// NewTaxonomyFromNCBI parses nodes relationship from nodes.dmp
// from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz .
func NewTaxonomyFromNCBI(file string) (*Taxonomy, error) {
return NewTaxonomy(file, 1, 3)
}
// NewTaxonomy only loads nodes from nodes.dmp file.
func NewTaxonomy(file string, childColumn int, parentColumn int) (*Taxonomy, error) {
if childColumn < 1 || parentColumn < 1 {
return nil, ErrIllegalColumnIndex
}
maxColumns := maxInt(childColumn, parentColumn)
fh, err := xopen.Ropen(file)
if err != nil {
return nil, fmt.Errorf("taxdump: %s", err)
}
defer func() {
fh.Close()
}()
nodes := make(map[uint32]uint32, 1024)
n := maxColumns + 1
childColumn--
parentColumn--
items := make([]string, n)
scanner := bufio.NewScanner(fh)
var _child, _parent int
var child, parent uint32
var maxTaxid uint32
var root uint32
for scanner.Scan() {
stringSplitN(scanner.Text(), "\t", n, &items)
if len(items) < maxColumns {
continue
}
_child, err = strconv.Atoi(items[childColumn])
if err != nil {
continue
}
_parent, err = strconv.Atoi(items[parentColumn])
if err != nil {
continue
}
child, parent = uint32(_child), uint32(_parent)
// ----------------------------------
nodes[child] = parent
if child == parent {
root = child
}
if child > maxTaxid {
maxTaxid = child
}
}
if err := scanner.Err(); err != nil {
return nil, fmt.Errorf("taxdump: %s", err)
}
return &Taxonomy{file: file, Nodes: nodes, rootNode: root, maxTaxid: maxTaxid}, nil
}
// NewTaxonomyWithRankFromNCBI parses Taxonomy from nodes.dmp
// from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz .
func NewTaxonomyWithRankFromNCBI(file string) (*Taxonomy, error) {
return NewTaxonomyWithRank(file, 1, 3, 5)
}
// NewTaxonomyWithRank loads nodes and ranks from nodes.dmp file.
func NewTaxonomyWithRank(file string, childColumn int, parentColumn int, rankColumn int) (*Taxonomy, error) {
if childColumn < 1 || parentColumn < 1 || rankColumn < 1 {
return nil, ErrIllegalColumnIndex
}
maxColumns := maxInt(childColumn, parentColumn, rankColumn)
taxid2rankid := make(map[uint32]uint8, 1024)
ranks := make([]string, 0, 128)
rank2rankid := make(map[string]int, 128)
ranksMap := make(map[string]interface{}, 128)
fh, err := xopen.Ropen(file)
if err != nil {
return nil, fmt.Errorf("taxdump: %s", err)
}
defer func() {
fh.Close()
}()
nodes := make(map[uint32]uint32, 1024)
n := maxColumns + 1
childColumn--
parentColumn--
rankColumn--
items := make([]string, n)
scanner := bufio.NewScanner(fh)
var _child, _parent int
var child, parent uint32
var maxTaxid uint32
var rank string
var ok bool
var rankid int
var root uint32
for scanner.Scan() {
stringSplitN(scanner.Text(), "\t", n, &items)
if len(items) < maxColumns {
continue
}
_child, err = strconv.Atoi(items[childColumn])
if err != nil {
continue
}
_parent, err = strconv.Atoi(items[parentColumn])
if err != nil {
continue
}
child, parent, rank = uint32(_child), uint32(_parent), items[rankColumn]
// ----------------------------------
nodes[child] = parent
if child == parent {
root = child
}
if child > maxTaxid {
maxTaxid = child
}
if rankid, ok = rank2rankid[rank]; ok {
taxid2rankid[child] = uint8(rankid)
} else {
ranks = append(ranks, rank)
if len(ranks) > 255 {
return nil, ErrTooManyRanks
}
rank2rankid[rank] = len(ranks) - 1
taxid2rankid[child] = uint8(len(ranks) - 1)
ranksMap[rank] = struct{}{}
}
}
if err := scanner.Err(); err != nil {
return nil, fmt.Errorf("taxdump: %s", err)
}
return &Taxonomy{file: file, Nodes: nodes, rootNode: root, maxTaxid: maxTaxid,
taxid2rankid: taxid2rankid, ranks: ranks, hasRanks: true, Ranks: ranksMap}, nil
}
// TaxId checks if a TaxId is valid in the database.
// If being merged, the new TaxId will be returned.
// If the TaxId is not found or deleted, false will be returned.
func (t *Taxonomy) TaxId(taxid uint32) (uint32, bool) {
_, ok := t.Nodes[taxid]
if ok {
return taxid, true
}
// check if it was merged
var newtaxid uint32
if newtaxid, ok = t.MergeNodes[taxid]; ok {
return newtaxid, true
}
// // taxid not found, check if it was deleted
// if _, ok = t.DelNodes[taxid]; ok {
// return taxid, false
// }
// not found
return taxid, false
}
// Name returns the name of a TaxId.
// If being merged, the name of the new TaxId will be returned.
// If the TaxId is not found or deleted, empty will be returned.
func (t *Taxonomy) Name(taxid uint32) string {
name, ok := t.Names[taxid]
if ok {
return name
}
// check if it was merged
var newtaxid uint32
if newtaxid, ok = t.MergeNodes[taxid]; ok {
return t.Names[newtaxid]
}
return ""
}
// Rank returns the rank of a taxid.
// If being merged, the rank of the new TaxId will be returned.
// If the TaxId is not found or deleted, empty will be returned.
func (t *Taxonomy) Rank(taxid uint32) string {
if !t.hasRanks {
panic(ErrRankNotLoaded)
}
if i, ok := t.taxid2rankid[taxid]; ok {
return t.ranks[int(i)]
}
if newTaxid, ok := t.MergeNodes[taxid]; ok { // merged
if i, ok := t.taxid2rankid[newTaxid]; ok {
return t.ranks[int(i)]
}
}
return "" // taxid not found or deleted
}
// AtOrBelowRank returns whether a taxid is at or below one rank.
func (t *Taxonomy) AtOrBelowRank(taxid uint32, rank string) bool {
if !t.hasRanks {
panic(ErrRankNotLoaded)
}
var ok bool
var i uint8
rank = strings.ToLower(rank)
if _, ok = t.Ranks[rank]; !ok {
return false
}
if i, ok = t.taxid2rankid[taxid]; ok {
if rank == t.ranks[int(i)] {
return true
}
}
// continue searching towards to root node
var child, parent, newtaxid uint32
child = taxid
for {
parent, ok = t.Nodes[child]
if !ok { // taxid not found
// // check if it was deleted
// if _, ok = t.DelNodes[child]; ok {
// return false
// }
// check if it was merged
if newtaxid, ok = t.MergeNodes[child]; ok {
child = newtaxid
if rank == t.ranks[t.taxid2rankid[child]] {
return true
}
parent = t.Nodes[child]
} else { // not found
return false
}
}
if parent == 1 {
break
}
if rank == t.ranks[t.taxid2rankid[parent]] {
return true
}
child = parent
}
return false
}
// LoadNamesFromNCBI loads scientific names from NCBI names.dmp
func (t *Taxonomy) LoadNamesFromNCBI(file string) error {
return t.LoadNames(file, 1, 3, 7, "scientific name")
}
// LoadNames loads names.
func (t *Taxonomy) LoadNames(file string, taxidColumn int, nameColumn int, typeColumn int, _type string) error {
if taxidColumn < 1 || nameColumn < 1 || typeColumn < 1 {
return ErrIllegalColumnIndex
}
maxColumns := maxInt(nameColumn, nameColumn, typeColumn)
fh, err := xopen.Ropen(file)
if err != nil {
return fmt.Errorf("taxdump: %s", err)
}
defer func() {
fh.Close()
}()
m := make(map[uint32]string, 1024)
n := maxColumns + 1
taxidColumn--
nameColumn--
typeColumn--
filterByType := _type != ""
items := make([]string, n)
scanner := bufio.NewScanner(fh)
var taxid uint64
for scanner.Scan() {
stringSplitN(scanner.Text(), "\t", n, &items)
if len(items) < maxColumns {
continue
}
if filterByType && items[typeColumn] != _type {
continue
}
taxid, err = strconv.ParseUint(items[taxidColumn], 10, 32)
if err != nil {
continue
}
m[uint32(taxid)] = items[nameColumn]
}
if err := scanner.Err(); err != nil {
return fmt.Errorf("taxdump: %s", err)
}
t.Names = m
t.hasNames = true
return nil
}
// LoadMergedNodesFromNCBI loads merged nodes from NCBI merged.dmp.
func (t *Taxonomy) LoadMergedNodesFromNCBI(file string) error {
return t.LoadMergedNodes(file, 1, 3)
}
// LoadMergedNodes loads merged nodes.
func (t *Taxonomy) LoadMergedNodes(file string, oldColumn int, newColumn int) error {
if oldColumn < 1 || newColumn < 1 {
return ErrIllegalColumnIndex
}
maxColumns := maxInt(oldColumn, newColumn)
fh, err := xopen.Ropen(file)
if err != nil {
if err == xopen.ErrNoContent {
return nil
}
return fmt.Errorf("taxdump: %s", err)
}
defer func() {
fh.Close()
}()
m := make(map[uint32]uint32, 1024)
n := maxColumns + 1
oldColumn--
newColumn--
items := make([]string, n)
scanner := bufio.NewScanner(fh)
var from, to int
for scanner.Scan() {
stringSplitN(scanner.Text(), "\t", n, &items)
if len(items) < maxColumns {
continue
}
from, err = strconv.Atoi(items[oldColumn])
if err != nil {
continue
}
to, err = strconv.Atoi(items[newColumn])
if err != nil {
continue
}
m[uint32(from)] = uint32(to)
}
if err := scanner.Err(); err != nil {
return fmt.Errorf("taxdump: %s", err)
}
t.MergeNodes = m
t.hasMergeNodes = true
return nil
}
// LoadDeletedNodesFromNCBI loads deleted nodes from NCBI delnodes.dmp.
func (t *Taxonomy) LoadDeletedNodesFromNCBI(file string) error {
return t.LoadDeletedNodes(file, 1)
}
// LoadDeletedNodes loads deleted nodes.
func (t *Taxonomy) LoadDeletedNodes(file string, column int) error {
if column < 1 {
return ErrIllegalColumnIndex
}
fh, err := xopen.Ropen(file)
if err != nil {
if err == xopen.ErrNoContent {
return nil
}
return fmt.Errorf("taxdump: %s", err)
}
defer func() {
fh.Close()
}()
m := make(map[uint32]struct{}, 1024)
maxColumns := column
n := maxColumns + 1
column--
items := make([]string, n)
scanner := bufio.NewScanner(fh)
var id int
for scanner.Scan() {
stringSplitN(scanner.Text(), "\t", n, &items)
if len(items) < maxColumns {
continue
}
id, err = strconv.Atoi(items[column])
if err != nil {
continue
}
m[uint32(id)] = struct{}{}
}
if err := scanner.Err(); err != nil {
return fmt.Errorf("taxdump: %s", err)
}
t.DelNodes = m
t.hasDelNodes = true
return nil
}
// MaxTaxid returns maximum taxid
func (t *Taxonomy) MaxTaxid() uint32 {
return t.maxTaxid
}
// CacheLCA tells to cache every LCA query result
func (t *Taxonomy) CacheLCA() {
t.cacheLCA = true
}
// LCA returns the Lowest Common Ancestor of two nodes, 0 for unknown taxid.
func (t *Taxonomy) LCA(a uint32, b uint32) uint32 {
if a == 0 || b == 0 {
return 0
}
if a == b {
return a
}
// check cache
var ok bool
var query uint64
var tmp interface{}
if t.cacheLCA {
query = pack2uint32(a, b)
tmp, ok = t.lcaCache.Load(query)
if ok {
return tmp.(uint32)
}
}
mA := make(map[uint32]struct{}, 16)
var child, parent, newTaxid uint32
var flag bool
child = a
for {
parent, ok = t.Nodes[child]
if !ok {
flag = false
if newTaxid, ok = t.MergeNodes[child]; ok { // merged
child = newTaxid // update child
parent, ok = t.Nodes[child]
if ok {
flag = true
}
}
if !flag {
if t.cacheLCA {
t.lcaCache.Store(query, uint32(0))
}
return 0
}
}
if parent == child { // root
mA[parent] = struct{}{}
break
}
if parent == b { // b is ancestor of a
if t.cacheLCA {
t.lcaCache.Store(query, b)
}
return b
}
mA[parent] = struct{}{}
child = parent
}
child = b
for {
parent, ok = t.Nodes[child]
if !ok {
flag = false
if newTaxid, ok = t.MergeNodes[child]; ok { // merged
child = newTaxid // update child
parent, ok = t.Nodes[child]
if ok {
flag = true
}
}
if !flag {
if t.cacheLCA {
t.lcaCache.Store(query, uint32(0))
}
return 0
}
}
if parent == child { // root
break
}
if parent == a { // a is ancestor of b
if t.cacheLCA {
t.lcaCache.Store(query, a)
}
return a
}
if _, ok = mA[parent]; ok {
if t.cacheLCA {
t.lcaCache.Store(query, parent)
}
return parent
}
child = parent
}
return t.rootNode
}
// LineageNames returns nodes' names of the the complete lineage.
func (t *Taxonomy) LineageNames(taxid uint32) []string {
taxids := t.LineageTaxIds(taxid)
if taxids == nil {
return nil
}
if !t.hasNames {
panic(ErrNamesNotLoaded)
}
names := make([]string, len(taxids))
for i, tax := range taxids {
names[i] = t.Names[tax]
}
return names
}
// LineageTaxIds returns nodes' taxid of the the complete lineage.
func (t *Taxonomy) LineageTaxIds(taxid uint32) []uint32 {
var child, parent, newtaxid uint32
var ok bool
child = taxid
list := make([]uint32, 0, 16)
for {
parent, ok = t.Nodes[child]
if !ok { // taxid not found
// // check if it was deleted
// if _, ok = t.DelNodes[child]; ok {
// return nil
// }
// check if it was merged
if newtaxid, ok = t.MergeNodes[child]; ok {
child = newtaxid
parent = t.Nodes[child]
} else { // not found
return nil
}
}
list = append(list, child)
if parent == 1 {
break
}
child = parent
}
// reversing
for i, j := 0, len(list)-1; i < j; i, j = i+1, j-1 {
list[i], list[j] = list[j], list[i]
}
return list
}
func pack2uint32(a uint32, b uint32) uint64 {
if a < b {
return (uint64(a) << 32) | uint64(b)
}
return (uint64(b) << 32) | uint64(a)
}
func minInt(a int, vals ...int) int {
min := a
for _, v := range vals {
if v < min {
min = v
}
}
return min
}
func maxInt(a int, vals ...int) int {
min := a
for _, v := range vals {
if v > min {
min = v
}
}
return min
}
func stringSplitN(s string, sep string, n int, a *[]string) {
if a == nil {
tmp := make([]string, n)
a = &tmp
}
n--
i := 0
for i < n {
m := strings.Index(s, sep)
if m < 0 {
break
}
(*a)[i] = s[:m]
s = s[m+len(sep):]
i++
}
(*a)[i] = s
(*a) = (*a)[:i+1]
}
bio-0.13.3/taxdump/taxonomy_test.go 0000664 0000000 0000000 00000002721 14573550650 0017311 0 ustar 00root root 0000000 0000000 // Copyright © 2018-2021 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package taxdump
import (
"testing"
)
func TestPackTwoTaxids(t *testing.T) {
type Test struct {
a, b uint32
c uint64
}
tests := []Test{
{0, 0, 0},
{1, 1, 1<<32 + 1},
{2, 1, 1<<32 + 2},
}
for _, test := range tests {
c := pack2uint32(test.a, test.b)
if c != test.c {
t.Errorf("pack2uint32 error: %d != %d ", c, test.c)
}
}
}
bio-0.13.3/util/ 0000775 0000000 0000000 00000000000 14573550650 0013336 5 ustar 00root root 0000000 0000000 bio-0.13.3/util/README.md 0000664 0000000 0000000 00000000221 14573550650 0014610 0 ustar 00root root 0000000 0000000 # util
Some utilities
- LengthStats: caculating statistics of sequence length, including, Min, Max, Mean, Median, N50, L50, Q1, Q2, Q3, et al.
bio-0.13.3/util/length-stats.go 0000664 0000000 0000000 00000016436 14573550650 0016314 0 ustar 00root root 0000000 0000000 package util
import (
"math"
"github.com/twotwotwo/sorts"
)
// LengthStats accepts sequence lengths and calculate N50 et al..
type LengthStats struct {
lens map[uint64]uint64
sum uint64
count uint64
min, max uint64
counts [][2]uint64 // length and it's number
accCounts [][2]uint64 // accumulative count
// accLens [][2]uint64 // accumulative length
sorted bool
n50Calculated bool
l50 int
nXCalculated bool
lX int
}
// NewLengthStats initializes a LengthStats
func NewLengthStats() *LengthStats {
return &LengthStats{lens: make(map[uint64]uint64, 256), min: 1<<64 - 1}
}
// Add adds a new length
func (stats *LengthStats) Add(length uint64) {
stats.count++
stats.sum += length
stats.lens[length]++
if length > stats.max {
stats.max = length
}
if length < stats.min {
stats.min = length
}
stats.sorted = false
}
type lengthCount [][2]uint64
func (lc lengthCount) Len() int { return len(lc) }
func (lc lengthCount) Less(i, j int) bool { return lc[i][0] < lc[j][0] }
func (lc lengthCount) Swap(i, j int) { lc[i], lc[j] = lc[j], lc[i] }
func (stats *LengthStats) sort() {
if len(stats.lens) == 0 {
stats.sorted = true
return
}
stats.counts = make([][2]uint64, 0, len(stats.lens))
for length, count := range stats.lens {
stats.counts = append(stats.counts, [2]uint64{length, count})
}
// sort.Slice(stats.counts, func(i, j int) bool { return stats.counts[i][0] < stats.counts[j][0] })
sorts.Quicksort(lengthCount(stats.counts))
stats.accCounts = make([][2]uint64, len(stats.lens))
stats.accCounts[0] = [2]uint64{stats.counts[0][0], stats.counts[0][1]}
if len(stats.counts) > 1 {
for i, data := range stats.counts[1:] {
stats.accCounts[i+1] = [2]uint64{data[0], data[1] + stats.accCounts[i][1]}
}
}
// stats.accLens = make([][2]uint64, len(stats.lens))
// for i, data := range stats.counts {
// if i == 0 {
// stats.accLens[i] = [2]uint64{data[0], data[0] * data[1]}
// } else {
// stats.accLens[i] = [2]uint64{data[0], data[0]*data[1] + stats.accLens[i-1][1]}
// }
// }
stats.sorted = true
}
// Count returns number of elements
func (stats *LengthStats) Count() uint64 {
return stats.count
}
// Min returns the minimum length
func (stats *LengthStats) Min() uint64 {
if stats.count == 0 {
return 0
}
return stats.min
}
// Max returns the maxinimum length
func (stats *LengthStats) Max() uint64 {
return stats.max
}
// Sum returns the length sum
func (stats *LengthStats) Sum() uint64 {
return stats.sum
}
// Mean returns mean
func (stats *LengthStats) Mean() float64 {
return float64(stats.sum) / float64(stats.count)
}
// Q2 returns Q2
func (stats *LengthStats) Q2() float64 {
return stats.Median()
}
// Median returns median
func (stats *LengthStats) Median() float64 {
if !stats.sorted {
stats.sort()
}
if len(stats.counts) == 0 {
return 0
}
if len(stats.counts) == 1 {
return float64(stats.counts[0][0])
}
even := stats.count&1 == 0 // %2 == 0
var iMedianL, iMedianR uint64 // 0-based
if even {
iMedianL = uint64(stats.count/2) - 1 // 3
iMedianR = uint64(stats.count / 2) // 4
} else {
iMedianL = uint64(stats.count / 2)
}
return stats.getValue(even, iMedianL, iMedianR)
}
// Q1 returns Q1
func (stats *LengthStats) Q1() float64 {
if !stats.sorted {
stats.sort()
}
if len(stats.counts) == 0 {
return 0
}
if len(stats.counts) == 1 {
return float64(stats.counts[0][0])
}
even := stats.count&1 == 0 // %2 == 0
var iMedianL, iMedianR uint64 // 0-based
var n uint64
if even {
n = stats.count / 2
} else {
n = (stats.count + 1) / 2
}
even = n%2 == 0
if even {
iMedianL = uint64(n/2) - 1
iMedianR = uint64(n / 2)
} else {
iMedianL = uint64(n / 2)
}
return stats.getValue(even, iMedianL, iMedianR)
}
// Q3 returns Q3
func (stats *LengthStats) Q3() float64 {
if !stats.sorted {
stats.sort()
}
if len(stats.counts) == 0 {
return 0
}
if len(stats.counts) == 1 {
return float64(stats.counts[0][0])
}
even := stats.count&1 == 0 // %2 == 0
var iMedianL, iMedianR uint64 // 0-based
var mean, n uint64
if even {
n = stats.count / 2
mean = n
} else {
n = (stats.count + 1) / 2
mean = stats.count / 2
}
even = n%2 == 0
if even {
iMedianL = uint64(n/2) - 1 + mean
iMedianR = uint64(n/2) + mean
} else {
iMedianL = uint64(n/2) + mean
}
return stats.getValue(even, iMedianL, iMedianR)
}
func (stats *LengthStats) getValue(even bool, iMedianL uint64, iMedianR uint64) float64 {
var accCount uint64
var flag bool
var prev uint64
for _, data := range stats.accCounts {
accCount = data[1]
if flag {
// the middle two having different length.
// example: 1, 2, 3, 4 or 1, 2
return float64(data[0]+prev) / 2
}
if accCount >= iMedianL+1 {
if even {
if accCount >= iMedianR+1 {
// having >=2 of same length in the middle.
// example: 2, 2, 2, 3, 3, 4, 8, 8
return float64(data[0])
}
flag = true
prev = data[0]
} else {
// right here
return float64(data[0])
}
}
}
// never happen
// panic("bio/util: should never happen")
return 0
}
func (stats *LengthStats) Percentile(percent float64) float64 {
if percent <= 0 || percent > 100 {
panic("invalid percentile")
}
if !stats.sorted {
stats.sort()
}
if len(stats.counts) == 0 {
return 0
}
if len(stats.counts) == 1 {
return float64(stats.counts[0][0])
}
i0 := float64(stats.count) * percent / 100
i := math.Floor(i0)
even := math.Abs(i0-i) > 0.001
var iMedianL, iMedianR uint64 // 0-based
if even {
iMedianL = uint64(i) - 1
iMedianR = uint64(i)
} else {
iMedianL = uint64(i - 1)
}
return stats.getValue(even, iMedianL, iMedianR)
}
// N50 returns N50
func (stats *LengthStats) N50() uint64 {
if !stats.sorted {
stats.sort()
}
if len(stats.counts) == 0 {
return 0
}
if len(stats.counts) == 1 {
stats.l50 = 1
return stats.counts[0][0]
}
var sumLen float64
var data [2]uint64
var halfSum = float64(stats.sum) / 2
for i := len(stats.counts) - 1; i >= 0; i-- {
data = stats.counts[i]
sumLen += float64(data[0] * data[1])
if sumLen >= halfSum {
stats.l50 = len(stats.counts) - i
stats.n50Calculated = true
return data[0]
}
}
// never happen
// panic("bio/util: should never happen")
return 0
}
// NX returns something like N50, where X could be a number in the range of [0, 100]
func (stats *LengthStats) NX(n float64) uint64 {
if n < 0 || n > 100 {
panic("NX: where X should be in range of [0, 100]")
}
if !stats.sorted {
stats.sort()
}
if len(stats.counts) == 0 {
return 0
}
if len(stats.counts) == 1 {
return stats.counts[0][0]
}
var sumLen float64
var data [2]uint64
var boundary = float64(stats.sum) * n / 100
for i := len(stats.counts) - 1; i >= 0; i-- {
data = stats.counts[i]
sumLen += float64(data[0] * data[1])
if sumLen >= boundary {
stats.lX = i + 1
stats.nXCalculated = true
return data[0]
}
}
// never happen
// panic("bio/util: should never happen")
return 0
}
// L50 returns L50
func (stats *LengthStats) L50() int {
if !stats.sorted {
stats.N50()
}
if !stats.n50Calculated {
stats.N50()
}
return stats.l50
}
// LX returns something like L50, where X could be a number in the range of [0, 100]
func (stats *LengthStats) LX(n float64) int {
if !stats.sorted {
stats.NX(n)
}
if !stats.nXCalculated {
stats.NX(n)
}
return stats.lX
}
bio-0.13.3/util/length-stats_test.go 0000664 0000000 0000000 00000004376 14573550650 0017353 0 ustar 00root root 0000000 0000000 package util
import (
"math/rand"
"testing"
)
type testCaseLengthStats struct {
data []uint64
q1, median, q3 float64
n50 uint64
l50 int
min, max uint64
}
var cases = []testCaseLengthStats{
testCaseLengthStats{
data: []uint64{},
median: 0,
q1: 0,
q3: 0,
n50: 0,
l50: 0,
min: 0,
max: 0,
},
testCaseLengthStats{
data: []uint64{2},
median: 2,
q1: 2,
q3: 2,
n50: 2,
l50: 1,
min: 2,
max: 2,
},
testCaseLengthStats{
data: []uint64{1, 2},
median: 1.5,
q1: 1,
q3: 2,
n50: 2,
l50: 1,
min: 1,
max: 2,
},
testCaseLengthStats{
data: []uint64{1, 2, 3},
median: 2,
q1: 1.5,
q3: 2.5,
n50: 3,
l50: 1,
min: 1,
max: 3,
},
testCaseLengthStats{
data: []uint64{1, 2, 3, 4},
median: 2.5,
q1: 1.5,
q3: 3.5,
n50: 3,
l50: 2,
min: 1,
max: 4,
},
testCaseLengthStats{
data: []uint64{2, 3, 4, 5, 6, 7, 8, 9},
median: 5.5,
q1: 3.5,
q3: 7.5,
n50: 7,
l50: 3,
min: 2,
max: 9,
},
}
func Test(t *testing.T) {
for i, _case := range cases {
rand.Shuffle(len(_case.data), func(i, j int) {
_case.data[i], _case.data[j] = _case.data[j], _case.data[i]
})
stats := NewLengthStats()
for _, l := range _case.data {
stats.Add(l)
}
if stats.Count() != uint64(len(_case.data)) {
t.Errorf("case %d: count mismatch", i)
}
min := stats.Min()
if min != _case.min {
t.Errorf("case %d: min mismatch: %d != %d", i, min, _case.min)
}
max := stats.Max()
if max != _case.max {
t.Errorf("case %d: max mismatch: %d != %d", i, max, _case.max)
}
median := stats.Median()
if median != _case.median {
t.Errorf("case %d: median mismatch: %f != %f", i, median, _case.median)
}
q1 := stats.Q1()
if q1 != _case.q1 {
t.Errorf("case %d: q1 mismatch: %f != %f", i, q1, _case.q1)
}
q3 := stats.Q3()
if q1 != _case.q1 {
t.Errorf("case %d: q3 mismatch: %f != %f", i, q3, _case.q3)
}
n50 := stats.N50()
if n50 != _case.n50 {
t.Errorf("case %d: n50 mismatch: %d != %d", i, n50, _case.n50)
}
l50 := stats.L50()
if l50 != _case.l50 {
t.Errorf("case %d: l50 mismatch: %d != %d", i, l50, _case.l50)
}
}
}