pax_global_header00006660000000000000000000000064126563503510014520gustar00rootroot0000000000000052 comment=8c02053206a74f0c3ac4181b32735c04cec96df3 pymummer-0.7.0/000077500000000000000000000000001265635035100133775ustar00rootroot00000000000000pymummer-0.7.0/.gitignore000066400000000000000000000012431265635035100153670ustar00rootroot00000000000000# Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] # C extensions *.so # Distribution / packaging .Python env/ build/ develop-eggs/ dist/ downloads/ eggs/ lib/ lib64/ parts/ sdist/ var/ *.egg-info/ .installed.cfg *.egg # PyInstaller # Usually these files are written by a python script from a template # before PyInstaller builds the exe, so as to inject date/other infos into it. *.manifest *.spec # Installer logs pip-log.txt pip-delete-this-directory.txt # Unit test / coverage reports htmlcov/ .tox/ .coverage .cache nosetests.xml coverage.xml # Translations *.mo *.pot # Django stuff: *.log # Sphinx documentation docs/_build/ # PyBuilder target/ pymummer-0.7.0/.travis.yml000066400000000000000000000003711265635035100155110ustar00rootroot00000000000000language: python addons: apt: packages: - g++ - python-dev cache: directories: - "build" - "$HOME/.cache/pip" python: - "3.3" - "3.4" sudo: false install: - "source ./install_dependencies.sh" script: "python setup.py test" pymummer-0.7.0/AUTHORS000066400000000000000000000001171265635035100144460ustar00rootroot00000000000000Martin Hunt (path-help@sanger.ac.uk) Nishadi De Silva (path-help@sanger.ac.uk) pymummer-0.7.0/LICENSE000066400000000000000000001044621265635035100144130ustar00rootroot00000000000000GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . pymummer-0.7.0/README.md000066400000000000000000000040721265635035100146610ustar00rootroot00000000000000pymummer ======== Python3 wrapper for running MUMmer and parsing the output. [![Build Status](https://travis-ci.org/sanger-pathogens/pymummer.svg?branch=master)](https://travis-ci.org/sanger-pathogens/pymummer) Installation ------------ ###Homebrew/LinuxBrew### ``` brew tap homebrew/python brew install pymummer ``` ##Pip ###Pre-requisites### The MUMmer package must be installed. Instructions to install MUMmer can be found [here](http://mummer.sourceforge.net/manual/#installation) ###Installation### Install with pip3 install pymummer Usage (for developers) ---------------------- Example showing how pymummer can be used to run nucmer on a fasta file and parse the output file to produce a set of alignment objects: from pymummer import coords_file, alignment, nucmer ... runner = nucmer.Runner(reference_file, query_file, results_file) runner.run() file_reader = coords_file.reader(results_file) alignments = [coord for coord in file_reader if not coord.is_self_hit()] #Remove self hits ... ###pymummer nucmer class### Wraps the `nucmer`, `delta-filter`, `show-coords` and `show-snps` commands. Arguments: __ref__ reference file __query__ query file __outfile__ output file __min\_id__ min\_id for delta-filter command (default None) __min\_length__ min\_length for delta-filter command (default None) __breaklen__ breaklen for nucmer command (nucmer's default is 200) __coords\_header__ print header in show-coords output (default True) __maxmatch__ maxmatch for nucmer (default False) __show\_snps__ run show-snps (default False) __snps\_header__ print header in show-snps output (default True) ###pymummer promer class### [TODO] ###pymummer coords_file class### Parses the nucmer output and populate an alignment object for each hit in the output ###pymummer alignment class### Check attributes of a hit, swap the reference and query, check if it's a self hit and so on Contact ------- Authors: Martin Hunt, Nishadi De Silva Affiliation: Wellcome Trust Sanger Institute, Hinxton, UK Email: path-help@sanger.ac.uk pymummer-0.7.0/install_dependencies.sh000066400000000000000000000023451265635035100201130ustar00rootroot00000000000000#!/bin/bash set -x set -e start_dir=$(pwd) MUMMER_VERSION="3.23" MUMMER_DOWNLOAD_URL="http://sourceforge.net/projects/mummer/files/mummer/${MUMMER_VERSION}/MUMmer${MUMMER_VERSION}.tar.gz/download" # Make an install location if [ ! -d 'build' ]; then mkdir build fi cd build build_dir=$(pwd) # DOWNLOAD ALL THE THINGS download () { url=$1 download_location=$2 if [ -e $download_location ]; then echo "Skipping download of $url, $download_location already exists" else echo "Downloading $url to $download_location" wget $url -O $download_location fi } download $MUMMER_DOWNLOAD_URL "mummer-${MUMMER_VERSION}.tgz" # Build all the things cd $build_dir ## Mummer mummer_dir=$(pwd)/MUMmer${MUMMER_VERSION} if [ ! -d $mummer_dir ]; then tar xzf mummer-${MUMMER_VERSION}.tgz fi cd $mummer_dir if [ -e "${mummer_dir}/mummer" ]; then echo "Already built Mummer; skipping build" else make check make cd ./src/tigr make fi cd $build_dir # Setup environment variables update_path () { new_dir=$1 export PATH=${PATH:-$new_dir} if [[ ! "$PATH" =~ (^|:)"${new_dir}"(:|$) ]]; then export PATH=${new_dir}:${PATH} fi } update_path ${mummer_dir} update_path ${mummer_dir}/src/tigr cd $start_dir set +x set +e pymummer-0.7.0/pymummer/000077500000000000000000000000001265635035100152525ustar00rootroot00000000000000pymummer-0.7.0/pymummer/__init__.py000066400000000000000000000002211265635035100173560ustar00rootroot00000000000000__all__ = [ 'alignment', 'coords_file', 'nucmer', 'snp', 'snp_file', 'syscall', 'variant', ] from pymummer import * pymummer-0.7.0/pymummer/alignment.py000066400000000000000000000163131265635035100176060ustar00rootroot00000000000000import pyfastaq from pymummer import variant class Error (Exception): pass class Alignment: def __init__(self, line): '''Constructs Alignment object from a line of show-coords -dTlro''' # nucmer: # [S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [LEN R] [LEN Q] [FRM] [TAGS] #1162 25768 24536 4 24607 24533 99.32 640851 24536 1 -1 ref qry [CONTAINS] # promer: #[S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [% SIM] [% STP] [LEN R] [LEN Q] [FRM] [TAGS] # 1 1398 4891054 4892445 1398 1392 89.55 93.18 0.21 1398 5349013 1 1 ref qry [CONTAINED] fields = line.rstrip().split('\t') try: self.ref_start = int(fields[0]) - 1 self.ref_end = int(fields[1]) - 1 self.qry_start = int(fields[2]) - 1 self.qry_end = int(fields[3]) - 1 self.hit_length_ref = int(fields[4]) self.hit_length_qry = int(fields[5]) self.percent_identity = float(fields[6]) if len(fields) >= 15: # promer has more fields self.ref_length = int(fields[9]) self.qry_length = int(fields[10]) self.frame = int(fields[11]) self.ref_name = fields[13] self.qry_name = fields[14] else: self.ref_length = int(fields[7]) self.qry_length = int(fields[8]) self.frame = int(fields[9]) self.ref_name = fields[11] self.qry_name = fields[12] except: raise Error('Error reading this nucmer line:\n' + line) def __eq__(self, other): return type(other) is type(self) and self.__dict__ == other.__dict__ def __hash__(self): return hash((self.ref_start, self.ref_end, self.qry_start, self.qry_end, self.hit_length_ref, self.hit_length_qry, self.percent_identity, self.ref_length, self.qry_length, self.frame, self.ref_name, self.qry_name)) def _swap(self): '''Swaps the alignment so that the reference becomes the query and vice-versa. Swaps their names, coordinates etc. The frame is not changed''' self.ref_start, self.qry_start = self.qry_start, self.ref_start self.ref_end, self.qry_end = self.qry_end, self.ref_end self.hit_length_ref, self.hit_length_qry = self.hit_length_qry, self.hit_length_ref self.ref_length, self.qry_length = self.qry_length, self.ref_length self.ref_name, self.qry_name = self.qry_name, self.ref_name def qry_coords(self): '''Returns a pyfastaq.intervals.Interval object of the start and end coordinates in the query sequence''' return pyfastaq.intervals.Interval(min(self.qry_start, self.qry_end), max(self.qry_start, self.qry_end)) def ref_coords(self): '''Returns a pyfastaq.intervals.Interval object of the start and end coordinates in the reference sequence''' return pyfastaq.intervals.Interval(min(self.ref_start, self.ref_end), max(self.ref_start, self.ref_end)) def on_same_strand(self): '''Returns true iff the direction of the alignment is the same in the reference and the query''' return (self.ref_start < self.ref_end) == (self.qry_start < self.qry_end) def is_self_hit(self): '''Returns true iff the alignment is of a sequence to itself: names and all coordinates are the same and 100 percent identity''' return self.ref_name == self.qry_name \ and self.ref_start == self.qry_start \ and self.ref_end == self.qry_end \ and self.percent_identity == 100 def reverse_query(self): '''Changes the coordinates as if the query sequence has been reverse complemented''' self.qry_start = self.qry_length - self.qry_start - 1 self.qry_end = self.qry_length - self.qry_end - 1 def reverse_reference(self): '''Changes the coordinates as if the reference sequence has been reverse complemented''' self.ref_start = self.ref_length - self.ref_start - 1 self.ref_end = self.ref_length - self.ref_end - 1 def __str__(self): '''Returns a tab delimited string containing the values of this alignment object''' return '\t'.join(str(x) for x in [self.ref_start + 1, self.ref_end + 1, self.qry_start + 1, self.qry_end + 1, self.hit_length_ref, self.hit_length_qry, '{0:.2f}'.format(self.percent_identity), self.ref_length, self.qry_length, self.frame, self.ref_name, self.qry_name]) def to_msp_crunch(self): '''Returns the alignment as a line in MSPcrunch format. The columns are space-separated and are: 1. score 2. percent identity 3. match start in the query sequence 4. match end in the query sequence 5. query sequence name 6. subject sequence start 7. subject sequence end 8. subject sequence name''' # we don't know the alignment score. Estimate it. This approximates 1 for a match. aln_score = int(self.percent_identity * 0.005 * (self.hit_length_ref + self.hit_length_qry)) return ' '.join(str(x) for x in [ aln_score, '{0:.2f}'.format(self.percent_identity), self.qry_start + 1, self.qry_end + 1, self.qry_name, self.ref_start + 1, self.ref_end + 1, self.ref_name ]) def qry_coords_from_ref_coord(self, ref_coord, variant_list): '''Given a reference position and a list of variants ([variant.Variant]), works out the position in the query sequence, accounting for indels. Returns a tuple: (position, True|False), where second element is whether or not the ref_coord lies in an indel. If it is, then returns the corresponding start position of the indel in the query''' if self.ref_coords().distance_to_point(ref_coord) > 0: raise Error('Cannot get query coord in qry_coords_from_ref_coord because given ref_coord ' + str(ref_coord) + ' does not lie in nucmer alignment:\n' + str(self)) indel_variant_indexes = [] for i in range(len(variant_list)): if variant_list[i].var_type not in {variant.INS, variant.DEL}: continue if variant_list[i].ref_start <= ref_coord <= variant_list[i].ref_end: return variant_list[i].qry_start, True elif variant_list[i].ref_start < ref_coord: indel_variant_indexes.append(i) distance = ref_coord - min(self.ref_start, self.ref_end) for i in indel_variant_indexes: if variant_list[i].var_type == variant.INS: distance += len(variant_list[i].qry_base) else: assert variant_list[i].var_type == variant.DEL distance -= len(variant_list[i].ref_base) if self.on_same_strand(): return min(self.qry_start, self.qry_end) + distance, False else: return max(self.qry_start, self.qry_end) - distance, False pymummer-0.7.0/pymummer/coords_file.py000066400000000000000000000033751265635035100201240ustar00rootroot00000000000000import pyfastaq from pymummer import alignment class Error (Exception): pass def reader(fname): '''Helper function to open the results file (coords file) and create alignment objects with the values in it''' f = pyfastaq.utils.open_file_read(fname) for line in f: if line.startswith('[') or (not '\t' in line): continue yield alignment.Alignment(line) pyfastaq.utils.close(f) def convert_to_msp_crunch(infile, outfile, ref_fai=None, qry_fai=None): '''Converts a coords file to a file in MSPcrunch format (for use with ACT, most likely). ACT ignores sequence names in the crunch file, and just looks at the numbers. To make a compatible file, the coords all must be shifted appropriately, which can be done by providing both the ref_fai and qry_fai options. Both or neither of these must be used, otherwise an error will be thrown.''' fai_files = {ref_fai, qry_fai} if None in fai_files and len(fai_files) != 1: print(fai_files) raise Error('Error in convert_to_msp_crunch. Must use both of ref_fai and qry_fai, or neither of them') if ref_fai is not None: assert qry_fai is not None ref_offsets = pyfastaq.tasks.length_offsets_from_fai(ref_fai) qry_offsets = pyfastaq.tasks.length_offsets_from_fai(qry_fai) file_reader = reader(infile) f_out = pyfastaq.utils.open_file_write(outfile) for aln in file_reader: if ref_fai is not None: aln.ref_start += ref_offsets[aln.ref_name] aln.ref_end += ref_offsets[aln.ref_name] aln.qry_start += qry_offsets[aln.qry_name] aln.qry_end += qry_offsets[aln.qry_name] print(aln.to_msp_crunch(), file=f_out) pyfastaq.utils.close(f_out) pymummer-0.7.0/pymummer/nucmer.py000066400000000000000000000072271265635035100171250ustar00rootroot00000000000000import os import tempfile import shutil import pyfastaq from pymummer import syscall class Error (Exception): pass class Runner: '''Handy reference for all the arguments needed for nucmer, delta-filter, show-coords, show-snps''' def __init__( self, ref, query, outfile, min_id=None, min_length=None, breaklen=None, coords_header=True, diagdiff=None, maxmatch=False, simplify=True, show_snps=False, snps_header=True, verbose=False, promer=False, ): self.qry = query self.ref = ref self.outfile = outfile self.min_id = min_id self.min_length = min_length self.breaklen = breaklen self.diagdiff = diagdiff self.coords_header = coords_header self.maxmatch = maxmatch self.simplify = simplify self.show_snps = show_snps self.snps_header = snps_header self.verbose = verbose self.use_promer = promer def _nucmer_command(self, ref, qry, outprefix): '''Construct the nucmer command''' if self.use_promer: command = 'promer' else: command = 'nucmer' command += ' -p ' + outprefix if self.breaklen is not None: command += ' -b ' + str(self.breaklen) if self.diagdiff is not None and not self.use_promer: command += ' -D ' + str(self.diagdiff) if self.maxmatch: command += ' --maxmatch' if not self.simplify and not self.use_promer: command += ' --nosimplify' return command + ' ' + ref + ' ' + qry def _delta_filter_command(self, infile, outfile): '''Construct delta-filter command''' command = 'delta-filter' if self.min_id is not None: command += ' -i ' + str(self.min_id) if self.min_length is not None: command += ' -l ' + str(self.min_length) return command + ' ' + infile + ' > ' + outfile def _show_coords_command(self, infile, outfile): '''Construct show-coords command''' command = 'show-coords -dTlro' if not self.coords_header: command += ' -H' return command + ' ' + infile + ' > ' + outfile def _show_snps_command(self, infile, outfile): command = 'show-snps -TClr' if not self.snps_header: command += ' -H' return command + ' ' + infile + ' > ' + outfile def _write_script(self, script_name, ref, qry, outfile): '''Write commands into a bash script''' f = pyfastaq.utils.open_file_write(script_name) print(self._nucmer_command(ref, qry, 'p'), file=f) print(self._delta_filter_command('p.delta', 'p.delta.filter'), file=f) print(self._show_coords_command('p.delta.filter', outfile), file=f) if self.show_snps: print(self._show_snps_command('p.delta.filter', outfile + '.snps'), file=f) pyfastaq.utils.close(f) def run(self): ''' Change to a temp directory Run bash script containing commands Place results in specified output file Clean up temp directory ''' qry = os.path.abspath(self.qry) ref = os.path.abspath(self.ref) outfile = os.path.abspath(self.outfile) tmpdir = tempfile.mkdtemp(prefix='tmp.run_nucmer.', dir=os.getcwd()) original_dir = os.getcwd() os.chdir(tmpdir) script = 'run_nucmer.sh' self._write_script(script, ref, qry, outfile) syscall.run('bash ' + script, verbose=self.verbose) os.chdir(original_dir) shutil.rmtree(tmpdir) pymummer-0.7.0/pymummer/snp.py000066400000000000000000000021651265635035100164300ustar00rootroot00000000000000class Error (Exception): pass class Snp: def __init__(self, line): #[P1] [SUB] [SUB] [P2] [BUFF] [DIST] [LEN R] [LEN Q] [FRM] [TAGS] #187 A C 269 187 187 654 853 1 1 ref_name qry_name try: l = line.rstrip().split('\t') self.ref_pos = int(l[0]) - 1 self.ref_base = l[1] self.qry_base = l[2] self.qry_pos = int(l[3]) - 1 self.ref_length = int(l[6]) self.qry_length = int(l[7]) self.ref_name = l[10] self.qry_name = l[11] except: raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line) def __eq__(self, other): return type(other) is type(self) and self.__dict__ == other.__dict__ def __str__(self): return '\t'.join([str(x) for x in [ self.ref_pos + 1, self.ref_base, self.qry_base, self.qry_pos + 1, self.ref_length, self.qry_length, self.ref_name, self.qry_name ]]) pymummer-0.7.0/pymummer/snp_file.py000066400000000000000000000010121265635035100174150ustar00rootroot00000000000000import pyfastaq from pymummer import snp, variant def reader(fname): f = pyfastaq.utils.open_file_read(fname) for line in f: if line.startswith('[') or (not '\t' in line): continue yield snp.Snp(line) pyfastaq.utils.close(f) def get_all_variants(fname): variants = [] fr = reader(fname) for nucmer_snp in fr: if len(variants) == 0 or not variants[-1].update_indel(nucmer_snp): variants.append(variant.Variant(nucmer_snp)) return variants pymummer-0.7.0/pymummer/syscall.py000066400000000000000000000013621265635035100173000ustar00rootroot00000000000000import os import sys import subprocess class Error (Exception): pass def decode(x): try: s = x.decode() except: return x return s def run(cmd, verbose=False): if verbose: print('Running command:', cmd, flush=True) try: output = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT) except subprocess.CalledProcessError as error: print('The following command failed with exit code', error.returncode, file=sys.stderr) print(cmd, file=sys.stderr) print('\nThe output was:\n', file=sys.stderr) print(error.output.decode(), file=sys.stderr) raise Error('Error running command:', cmd) if verbose: print(decode(output)) pymummer-0.7.0/pymummer/tests/000077500000000000000000000000001265635035100164145ustar00rootroot00000000000000pymummer-0.7.0/pymummer/tests/alignment_test.py000066400000000000000000000275761265635035100220240ustar00rootroot00000000000000import unittest import os import pyfastaq from pymummer import alignment, snp, variant modules_dir = os.path.dirname(os.path.abspath(alignment.__file__)) data_dir = os.path.join(modules_dir, 'tests', 'data') class TestNucmer(unittest.TestCase): def test_init_nucmer(self): '''test __init__ nucmer''' line = '\t'.join(['1', '100', '2', '200', '101', '202', '42.42', '123', '456', '-1', '0', 'ref', 'qry', '[FOO]']) a = alignment.Alignment(line) self.assertEqual(a.ref_start, 0) self.assertEqual(a.ref_end, 99) self.assertEqual(a.qry_start, 1) self.assertEqual(a.qry_end, 199) self.assertEqual(a.hit_length_ref, 101) self.assertEqual(a.hit_length_qry, 202) self.assertEqual(a.percent_identity, 42.42) self.assertEqual(a.ref_length, 123) self.assertEqual(a.qry_length, 456) self.assertEqual(a.frame, -1) self.assertEqual(a.ref_name, 'ref') self.assertEqual(a.qry_name, 'qry') def test_init_promer(self): '''test __init__ promer''' line = '\t'.join(['1', '1398', '4891054', '4892445', '1398', '1392', '89.55', '93.18', '0.21', '1398', '5349013', '1', '1', 'ref', 'qry', '[CONTAINED]']) a = alignment.Alignment(line) self.assertEqual(a.ref_start, 0) self.assertEqual(a.ref_end, 1397) self.assertEqual(a.qry_start, 4891053) self.assertEqual(a.qry_end, 4892444) self.assertEqual(a.hit_length_ref, 1398) self.assertEqual(a.hit_length_qry, 1392) self.assertEqual(a.percent_identity, 89.55) self.assertEqual(a.ref_length, 1398) self.assertEqual(a.qry_length, 5349013) self.assertEqual(a.frame, 1) self.assertEqual(a.ref_name, 'ref') self.assertEqual(a.qry_name, 'qry') def test_swap(self): ''' test swap''' l_in = ['1', '100', '2', '200', '101', '202', '42.42', '123', '456', '-1', '0', 'ref', 'qry'] l_out = ['2', '200', '1', '100', '202', '101', '42.42', '456', '123', '-1', '0', 'qry', 'ref'] a_in = alignment.Alignment('\t'.join(l_in)) a_in._swap() self.assertEqual(a_in, alignment.Alignment('\t'.join(l_out))) a_in._swap() self.assertEqual(a_in, alignment.Alignment('\t'.join(l_in))) def test_qry_coords(self): '''Test qry_coords''' hits = ['\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'qry']), '\t'.join(['1', '101', '100', '1', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'qry']) ] for h in hits: a = alignment.Alignment(h) self.assertEqual(pyfastaq.intervals.Interval(0,99), a.qry_coords()) def test_ref_coords(self): '''Test ref_coords''' hits = ['\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']), '\t'.join(['100', '1', '100', '1', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']) ] for h in hits: a = alignment.Alignment(h) self.assertEqual(pyfastaq.intervals.Interval(0,99), a.ref_coords()) def test_on_same_strand(self): '''test on_same_strand''' self.assertTrue(alignment.Alignment('\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref'])).on_same_strand()) self.assertTrue(alignment.Alignment('\t'.join(['100', '1', '100', '1', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref'])).on_same_strand()) self.assertFalse(alignment.Alignment('\t'.join(['1', '100', '100', '1', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref'])).on_same_strand()) self.assertFalse(alignment.Alignment('\t'.join(['100', '1', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref'])).on_same_strand()) def test_is_self_hit(self): '''Test is_self_hit''' tests = [('\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']), True), ('\t'.join(['1', '101', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']), False), ('\t'.join(['2', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']), False), ('\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref2']), False), ('\t'.join(['1', '100', '1', '100', '100', '100', '99.9', '1000', '1000', '1', '1', 'ref', 'ref']), False), ] for t in tests: a = alignment.Alignment(t[0]) self.assertEqual(a.is_self_hit(), t[1]) def test_reverse_reference(self): '''Test reverse_reference''' aln = alignment.Alignment('\t'.join(['100', '142', '1', '42', '43', '42', '100.00', '150', '100', '1', '1', 'ref', 'qry'])) expected = alignment.Alignment('\t'.join(['51', '9', '1', '42', '43', '42', '100.00', '150', '100', '1', '1', 'ref', 'qry'])) aln.reverse_reference() self.assertEqual(expected, aln) def test_reverse_query(self): '''Test reverse_query''' aln = alignment.Alignment('\t'.join(['100', '142', '1', '42', '43', '42', '100.00', '150', '100', '1', '1', 'ref', 'qry'])) expected = alignment.Alignment('\t'.join(['100', '142', '100', '59', '43', '42', '100.00', '150', '100', '1', '1', 'ref', 'qry'])) aln.reverse_query() self.assertEqual(expected, aln) def test_str(self): '''Test __str__''' l_in = ['1', '100', '2', '200', '101', '202', '42.42', '123', '456', '-1', '0', 'ref', 'qry'] # the 10th column (counting from zero) is ignored and so not output by __str__ l_out = l_in[:10] + l_in[11:] a = alignment.Alignment('\t'.join(l_in)) self.assertEqual(str(a), '\t'.join(l_out)) def test_to_msp_crunch(self): '''Test to_msp_crunch''' l_in = ['100', '110', '1', '10', '10', '11', '80.00', '123', '456', '-1', '0', 'ref', 'qry'] a = alignment.Alignment('\t'.join(l_in)) expected = '8 80.00 1 10 qry 100 110 ref' self.assertEqual(expected, a.to_msp_crunch()) def test_qry_coords_from_ref_coord_test_bad_ref_coord(self): '''Test qry_coords_from_ref_coord with bad ref coords''' aln = alignment.Alignment('\t'.join(['100', '200', '1', '100', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry'])) with self.assertRaises(alignment.Error): got = aln.qry_coords_from_ref_coord(98, []) with self.assertRaises(alignment.Error): got = aln.qry_coords_from_ref_coord(200, []) def test_qry_coords_from_ref_coord_test_same_strand(self): '''Test qry_coords_from_ref_coord on same strand''' aln = alignment.Alignment('\t'.join(['100', '200', '1', '101', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry'])) snp0 = snp.Snp('\t'.join(['140', 'A', 'T', '40', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # snp snp0 = variant.Variant(snp0) snp1 = snp.Snp('\t'.join(['140', 'A', '.', '40', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from qry snp2 = snp.Snp('\t'.join(['141', 'C', '.', '40', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from qry del1 = variant.Variant(snp1) del2 = variant.Variant(snp1) self.assertTrue(del2.update_indel(snp2)) snp3 = snp.Snp('\t'.join(['150', '.', 'A', '50', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from ref snp4 = snp.Snp('\t'.join(['150', '.', 'C', '51', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from ref snp5 = snp.Snp('\t'.join(['150', '.', 'G', '52', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from ref ins1 = variant.Variant(snp3) ins2 = variant.Variant(snp3) self.assertTrue(ins2.update_indel(snp4)) self.assertTrue(ins2.update_indel(snp5)) tests = [ (99, [], (0, False)), (100, [], (1, False)), (199, [], (100, False)), (119, [del1], (20, False)), (149, [], (50, False)), (149, [del1], (49, False)), (149, [del2], (48, False)), (159, [], (60, False)), (159, [ins1], (61, False)), (159, [ins2], (63, False)), (159, [del1, ins1], (60, False)), (159, [del1, ins2], (62, False)), (159, [del2, ins1], (59, False)), (159, [del2, ins2], (61, False)), (139, [del1], (39, True)), (139, [snp0], (40, False)), (149, [ins1], (49, True)), ] for ref_coord, variant_list, expected in tests: got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) self.assertEqual(expected, got) # if we reverse the direction of hit in query and reference, should get the same answer aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) self.assertEqual(expected, got) aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start def test_qry_coords_from_ref_coord_test_different_strand(self): '''Test qry_coords_from_ref_coord on different strand''' aln = alignment.Alignment('\t'.join(['100', '200', '101', '1', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry'])) snp0 = snp.Snp('\t'.join(['140', 'A', 'T', '40', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # snp snp0 = variant.Variant(snp0) snp1 = snp.Snp('\t'.join(['140', 'A', '.', '40', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from qry snp2 = snp.Snp('\t'.join(['141', 'C', '.', '40', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from qry del1 = variant.Variant(snp1) del2 = variant.Variant(snp1) self.assertTrue(del2.update_indel(snp2)) snp3 = snp.Snp('\t'.join(['150', '.', 'A', '50', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from ref snp4 = snp.Snp('\t'.join(['150', '.', 'C', '51', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from ref snp5 = snp.Snp('\t'.join(['150', '.', 'G', '52', 'x', 'x', '300', '300', 'x', 'x', 'ref', 'qry'])) # del from ref ins1 = variant.Variant(snp3) ins2 = variant.Variant(snp3) self.assertTrue(ins2.update_indel(snp4)) self.assertTrue(ins2.update_indel(snp5)) tests = [ (99, [], (100, False)), (100, [], (99, False)), (199, [], (0, False)), (119, [], (80, False)), (119, [del1], (80, False)), (149, [], (50, False)), (149, [del1], (51, False)), (149, [del2], (52, False)), (159, [], (40, False)), (159, [ins1], (39, False)), (159, [ins2], (37, False)), (159, [del1, ins1], (40, False)), (159, [del1, ins2], (38, False)), (159, [del2, ins1], (41, False)), (159, [del2, ins2], (39, False)), (139, [del1], (39, True)), (139, [snp0], (60, False)), (149, [ins1], (49, True)), ] for ref_coord, variant_list, expected in tests: got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) self.assertEqual(expected, got) # if we reverse the direction of hit in query and reference, should get the same answer aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) self.assertEqual(expected, got) aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start pymummer-0.7.0/pymummer/tests/coords_file_test.py000066400000000000000000000050721265635035100223210ustar00rootroot00000000000000import unittest import os import filecmp from pymummer import coords_file, alignment modules_dir = os.path.dirname(os.path.abspath(coords_file.__file__)) data_dir = os.path.join(modules_dir, 'tests', 'data') class TestCoordsFile(unittest.TestCase): def test_coords_file(self): '''test coords_file''' expected = [ '\t'.join(['61', '900', '1', '840', '840', '840', '99.76', '1000', '840', '1', '1', 'test_ref1', 'test_qry1', '[CONTAINS]']), '\t'.join(['62', '901', '2', '841', '841', '850', '99.66', '999', '839', '1', '1', 'test_ref2', 'test_qry2', '[CONTAINS]']), '\t'.join(['63', '902', '3', '842', '842', '860', '99.56', '998', '838', '1', '1', 'test_ref3', 'test_qry3', '[CONTAINS]']) ] expected = [alignment.Alignment(x) for x in expected] infiles = [os.path.join(data_dir, 'coords_file_test_with_header.coords'), os.path.join(data_dir, 'coords_file_test_no_header.coords')] for fname in infiles: fr = coords_file.reader(fname) alignments = [x for x in fr] self.assertEqual(alignments, expected) def test_convert_to_msp_crunch_no_offset(self): '''Test convert_to_msp_crunch with no offsets''' infile = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.coords') expected = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.no_offset.crunch') tmpfile = 'tmp.test_convert_to_msp_crunch_no_offset.crunch' coords_file.convert_to_msp_crunch(infile, tmpfile) self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) os.unlink(tmpfile) def test_convert_to_msp_crunch_with_offset(self): '''Test convert_to_msp_crunch with offsets''' infile = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.coords') ref_fai = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.ref.fa.fai') qry_fai = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.qry.fa.fai') expected = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.with_offset.crunch') tmpfile = 'tmp.test_convert_to_msp_crunch_with_offset.crunch' with self.assertRaises(coords_file.Error): coords_file.convert_to_msp_crunch(infile, tmpfile, ref_fai=ref_fai) coords_file.convert_to_msp_crunch(infile, tmpfile, qry_fai=qry_fai) coords_file.convert_to_msp_crunch(infile, tmpfile, ref_fai=ref_fai, qry_fai=qry_fai) self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) os.unlink(tmpfile) pymummer-0.7.0/pymummer/tests/data/000077500000000000000000000000001265635035100173255ustar00rootroot00000000000000pymummer-0.7.0/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.coords000066400000000000000000000007231265635035100305540ustar00rootroot00000000000000/Users/mh12/sanger-pathogens/pymummer/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa /Users/mh12/sanger-pathogens/pymummer/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa NUCMER [S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [LEN R] [LEN Q] [FRM] [TAGS] 1 420 1 420 420 420 99.76 420 420 1 1 ref1 qry1 [IDENTITY] 1 480 1 479 480 479 99.58 480 479 1 1 ref2 qry2 [IDENTITY] 61 420 1 360 360 360 99.44 500 360 1 1 ref3 qry3 [CONTAINS] pymummer-0.7.0/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.no_offset.crunch000066400000000000000000000001411265635035100325200ustar00rootroot00000000000000418 99.76 1 420 qry1 1 420 ref1 477 99.58 1 479 qry2 1 480 ref2 357 99.44 1 360 qry3 61 420 ref3 pymummer-0.7.0/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa000066400000000000000000000024221265635035100304610ustar00rootroot00000000000000>qry1 AACTTTCATACTGTAGTTATTGGCATCGTTGTAAAATTGCTCACCACGTCGCTCGTTCAT GATAATCTAAAGATCGCTAACGATTACTACCGGCAGCGGTTTATACGGACCAATCGTTGG TTCATTTTAATGTAGACCCAGAAATCGACTGCATTTCTGCAGCCCGGCCCGACGTGTTGA ACGGATGATCTTAGACAGAACGTCCTTGGGTCTATATCCGGCCACATATTTATTGGGCAG GGGAGTCAATTGGGGGCGTACCGAAATATCGTCTTTACGAGCGTCGGTGACGCACATGAC ATGGTCGACCCATAGCCTCAGCTTCTAGACGGTTGCACCAGCGCAAGACAAAACTCTCAA TTTTGTCTGGGTACCGAGATTGCGGAACCGGGGATATTGTAGAGCGGTGCACACGGCCTT >qry2 CTAGCGCAAGACCGACTCTGATTCATGGAGACAGGGCCAGACAGGGAAACGAGATTGAGC GATGCTGTCATTTTCGTAACGAGGATTGGTCGGGGACCGAGATCGTACACGTCTCCGAGC CCCCACAGTCGAGTACAAATGGCTTAATTTACTGACTTCTTCCTGTTACCGGCATGGTAT GCTGAGCCTGGCCCGCTCACTATTGGATATAGCCTGTGCGCTGGCGTACCGCTGTTCTAC CGGTTCCTCTTGAGGGTCAAAGGCCGGCTACCATCGTTAACTTATTAGCTTAGAGTAATG TAGGTTACGTGACGCTGGCCGGTTAGCGTTTCGAAGGATCGCAGGACTATAGTCAAAACT CGTGGACTTCTACCAGAACTATCGATGTTCACGATGACTACGTTCCTTCCGAATATTACA GTAAGGGATAGTCATGCCGGTTTAACATCATCTGTGTGTACGCAATGCAGTTTGGCACA >qry3 AGGTGCGACAGGATCTAACACCTGTACAGTAAGAAAGGGGCATATGATCGACCCCGGTTG CTCGTATGATAATCCCATTATTGTTATCTGAGGATCGTTATGCGGCAGTTCTAGTCCGAT AAAAGTTAGGTGAGTTGTGTTGGTAATCCTTCTCTAGGAGGCCTGGCGACTCCACTGAGC CCAGCGATGGGAGAGCTGGTCCCCCCAATATCGTGACTGAATTGGTAAGGTAGATATCTC CCAGATAGCCGCATACCGTCTGGCACCGTCGACCGAAAGAAATGTTCGCCTTGGCATGCT CAGATTGCATCTATACTTACTTGTATAGAACTGCCCGCGCCACCCAGAAGACAAACTAAT pymummer-0.7.0/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa.fai000066400000000000000000000000671265635035100312220ustar00rootroot00000000000000qry1 420 6 60 61 qry2 479 439 60 61 qry3 360 932 60 61 pymummer-0.7.0/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa000066400000000000000000000026421265635035100304260ustar00rootroot00000000000000>ref1 AACTTTCATACTGTAGTTATTGGCATCGTTGTAAAATTGCTCACCACGTCGCTCGTTCAT GATAATCTAAAGATCGCTAACGATTACTACCGGCAGCGGTTTATACGGACCAATCGTTGG TTCATTTTAATGTAGACCCAGAAATCGACTGCATTTCTGCAGCCCGGCCCGACGTGTTGA ACGGATGATCTTAGACAGAACGTCCTTGGGTCTATATCCGGCCACATATTTATTGGGCAG GGGTGTCAATTGGGGGCGTACCGAAATATCGTCTTTACGAGCGTCGGTGACGCACATGAC ATGGTCGACCCATAGCCTCAGCTTCTAGACGGTTGCACCAGCGCAAGACAAAACTCTCAA TTTTGTCTGGGTACCGAGATTGCGGAACCGGGGATATTGTAGAGCGGTGCACACGGCCTT >ref2 CTAGCGCAAGACCGACTCTGATTCATGGAGACAGGGCCAGACAGGGAAACGAGATTGAGC GATGCTGTCATTTTCGTAACGAGGATTGGTCGGGGACCGAGATCGTACACGTCTCCGAGC CCCCACAGTCGAGTACAAATGGCTTAATTTACTGACTTCTTCCTGTTACCGGCATGGTAT GCTGAGCCTGGCCCGCTCACTATTGGATATAGCCTGTGCGCTGGCGTACCGCTGTTCTAC CGGTACCTCTTGAGGGTCAAAGGCCGGCTACCATCGTTAACTTATTAGCTTAGAGTAATG TAGGTTACGTGACGCTGGCCGGTTAGCGTTTCGAAGGATCGCAGGACTATAGTCAAAACT CGTGGACTTCTACCAGAACTATCGATGTTCACGATGACTACGTTCCTTCCGAATATTACA GTATAGGGATAGTCATGCCGGTTTAACATCATCTGTGTGTACGCAATGCAGTTTGGCACA >ref3 ATTCAACGGGTAGGGTCATCAGATTTTTAGTACGAACGAACAATTCCCCATTCAATTCCG AGGTGCGACAGGATCTAACACCTGTACAGTAAGAAAGGGGCATATGATCGACCCCGGTTG CTCGTATGATAATCCCATTATTGTTATCTGAGGATCGTTATGCGGCAGTTCTAGTCCGAT CCAAGTTAGGTGAGTTGTGTTGGTAATCCTTCTCTAGGAGGCCTGGCGACTCCACTGAGC CCAGCGATGGGAGAGCTGGTCCCCCCAATATCGTGACTGAATTGGTAAGGTAGATATCTC CCAGATAGCCGCATACCGTCTGGCACCGTCGACCGAAAGAAATGTTCGCCTTGGCATGCT CAGATTGCATCTATACTTACTTGTATAGAACTGCCCGCGCCACCCAGAAGACAAACTAAT TTATTGTCGCTCAAACCTGTTTAGTTAATTCACCTTTGTAACCAGCTTACCCTCAATTGC GTATGTAACTCCTTGGCTGC pymummer-0.7.0/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa.fai000066400000000000000000000000671265635035100311630ustar00rootroot00000000000000ref1 420 6 60 61 ref2 480 439 60 61 ref3 500 933 60 61 pymummer-0.7.0/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.with_offset.crunch000066400000000000000000000001521265635035100330610ustar00rootroot00000000000000418 99.76 1 420 qry1 1 420 ref1 477 99.58 421 899 qry2 421 900 ref2 357 99.44 900 1259 qry3 961 1320 ref3 pymummer-0.7.0/pymummer/tests/data/coords_file_test_no_header.coords000066400000000000000000000003231265635035100260710ustar00rootroot0000000000000061 900 1 840 840 840 99.76 1000 840 1 1 test_ref1 test_qry1 [CONTAINS] 62 901 2 841 841 850 99.66 999 839 1 1 test_ref2 test_qry2 [CONTAINS] 63 902 3 842 842 860 99.56 998 838 1 1 test_ref3 test_qry3 [CONTAINS] pymummer-0.7.0/pymummer/tests/data/coords_file_test_with_header.coords000066400000000000000000000005061265635035100264330ustar00rootroot00000000000000/path/to/ref.fa /path/to/query.fa NUCMER [S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [LEN R] [LEN Q] [FRM] [TAGS] 61 900 1 840 840 840 99.76 1000 840 1 1 test_ref1 test_qry1 [CONTAINS] 62 901 2 841 841 850 99.66 999 839 1 1 test_ref2 test_qry2 [CONTAINS] 63 902 3 842 842 860 99.56 998 838 1 1 test_ref3 test_qry3 [CONTAINS] pymummer-0.7.0/pymummer/tests/data/nucmer_test_out.coords000066400000000000000000000001051265635035100237530ustar00rootroot0000000000000061 900 1 840 840 840 99.76 1000 840 1 1 test_ref test_qry [CONTAINS] pymummer-0.7.0/pymummer/tests/data/nucmer_test_out.coords.snps000066400000000000000000000001421265635035100247360ustar00rootroot00000000000000436 C . 375 2 375 1000 840 1 1 test_ref test_qry 438 . G 378 2 378 1000 840 1 1 test_ref test_qry pymummer-0.7.0/pymummer/tests/data/nucmer_test_qry.fa000066400000000000000000000015401265635035100230600ustar00rootroot00000000000000>test_qry GTAATCAAATAATCCACCGGATGAGGTATTTTCTCATCGGGGTGACTCTAACCACATCGT GTTTCTTCCTGAAGGCTCTAAGATGTCATGAGAACTCTTACTGTCTAGCTGAGGGGCTTG TGCACAACACTAGGATTGTGTCTTATGCTCTATTGGACAGCGAAAACTGCTGAAATTAAC GGGCCGTAACATACTATATTCTTCAAACCGAATTAACGTTCAGCCCCCGCTTGATTGCGA AATTAACTGGAATGCAACACCTTGCACTGGCCGTCCTGCGGTGGTGACCCTTTGAGGTAA ACACGTCGTCGACGCATTACAGTTGGGAGAAGCACACTCATGTTTCTAATAAAGCGCTCA CAGACGCGACCACTATAGCTCTAAAATACATCCCTCTAAGGTTCCATCTAGAAAGTGGCC CCCGCGACCGTCTACCGTGGTGGATGCAGGGAGTCACCTACGCGTCTTTTCGTGCTACCT AGGCATTTTTGCACTACCTAACTCCGTATTAAGGCCTTCGGAGAGGGCCGTCCCACTTCA ATGTGTGTGGTGGACTGTCCTCATGGGAAAAGCAAGTGTTTGACCGGTTGACACTAGTCC CGTTTATCTTCATGGGCGGGAGCGCGCATTCGTGACGGGGACACTTCTCGCCGTTTAGCC GGTGAGCTTATTAGGCCGATGGCGGGCCACCCTGATACGGGGGCCTATATGTCCACGAAT ATCAATTTCTGTATAACATTGGGCGCAGAAAACAGACTGGTCCAAATAAGATGAATCTAT AGCCCAGTGTGTTGCCTAAACGCTGAGCGAATAATTGGTCGCGCTCGGCGAGACCAGGGA pymummer-0.7.0/pymummer/tests/data/nucmer_test_ref.fa000066400000000000000000000020031265635035100230140ustar00rootroot00000000000000>test_ref TCAAGATCGTGCCCCGTTGATATCGCTGTTGCACAGGACTTTCTCCACCCTGATACCGCA GTAATCAAATAATCCACCGGATGAGGTATTTTCTCATCGGGGTGACTCTAACCACATCGT GTTTCTTCCTGAAGGCTCTAAGATGTCATGAGAACTCTTACTGTCTAGCTGAGGGGCTTG TGCACAACACTAGGATTGTGTCTTATGCTCTATTGGACAGCGAAAACTGCTGAAATTAAC GGGCCGTAACATACTATATTCTTCAAACCGAATTAACGTTCAGCCCCCGCTTGATTGCGA AATTAACTGGAATGCAACACCTTGCACTGGCCGTCCTGCGGTGGTGACCCTTTGAGGTAA ACACGTCGTCGACGCATTACAGTTGGGAGAAGCACACTCATGTTTCTAATAAAGCGCTCA CAGACGCGACCACTACTACTCTAAAATACATCCCTCTAAGGTTCCATCTAGAAAGTGGCC CCCGCGACCGTCTACCGTGGTGGATGCAGGGAGTCACCTACGCGTCTTTTCGTGCTACCT AGGCATTTTTGCACTACCTAACTCCGTATTAAGGCCTTCGGAGAGGGCCGTCCCACTTCA ATGTGTGTGGTGGACTGTCCTCATGGGAAAAGCAAGTGTTTGACCGGTTGACACTAGTCC CGTTTATCTTCATGGGCGGGAGCGCGCATTCGTGACGGGGACACTTCTCGCCGTTTAGCC GGTGAGCTTATTAGGCCGATGGCGGGCCACCCTGATACGGGGGCCTATATGTCCACGAAT ATCAATTTCTGTATAACATTGGGCGCAGAAAACAGACTGGTCCAAATAAGATGAATCTAT AGCCCAGTGTGTTGCCTAAACGCTGAGCGAATAATTGGTCGCGCTCGGCGAGACCAGGGA TTCTGGCAAGATCCTAACTCGGCCGTCAATGATGTTAAATCAACTCGGTGTGGCCCCAGC TTCGACACCAAAAGTTGTGATCACTACATAGCGTATCTCG pymummer-0.7.0/pymummer/tests/data/nucmer_test_write_script_no_snps.sh000066400000000000000000000001461265635035100265470ustar00rootroot00000000000000nucmer -p p ref qry delta-filter p.delta > p.delta.filter show-coords -dTlro p.delta.filter > outfile pymummer-0.7.0/pymummer/tests/data/nucmer_test_write_script_with_snps.sh000066400000000000000000000002241265635035100271030ustar00rootroot00000000000000nucmer -p p ref qry delta-filter p.delta > p.delta.filter show-coords -dTlro p.delta.filter > outfile show-snps -TClr p.delta.filter > outfile.snps pymummer-0.7.0/pymummer/tests/data/snp_file_test_get_all_variants.snps000066400000000000000000000004761265635035100264750ustar00rootroot00000000000000125 T . 124 1 124 500 497 1 1 ref1 qry1 126 A . 124 1 124 500 497 1 1 ref1 qry1 127 C . 124 1 124 500 497 1 1 ref1 qry1 386 C T 383 115 115 500 497 1 1 ref1 qry1 479 . G 480 0 22 500 504 1 1 ref2 qry2 479 . A 481 0 22 500 504 1 1 ref2 qry2 479 . T 482 0 22 500 504 1 1 ref2 qry2 479 . A 483 0 22 500 504 1 1 ref2 qry2 pymummer-0.7.0/pymummer/tests/data/snp_file_test_no_header.snps000066400000000000000000000001641265635035100250750ustar00rootroot00000000000000133 G . 122 1 122 500 489 1 1 ref qry 143 . C 131 1 132 500 489 1 1 ref qry 253 T A 242 120 242 500 489 1 1 ref qry pymummer-0.7.0/pymummer/tests/data/snp_file_test_with_header.snps000066400000000000000000000003351265635035100254340ustar00rootroot00000000000000/path/to/ref.fa /path/to/qry.fa NUCMER [P1] [SUB] [SUB] [P2] [BUFF] [DIST] [LEN R] [LEN Q] [FRM] [TAGS] 133 G . 122 1 122 500 489 1 1 ref qry 143 . C 131 1 132 500 489 1 1 ref qry 253 T A 242 120 242 500 489 1 1 ref qry pymummer-0.7.0/pymummer/tests/nucmer_test.py000066400000000000000000000103361265635035100213210ustar00rootroot00000000000000import unittest import os import filecmp from pymummer import nucmer modules_dir = os.path.dirname(os.path.abspath(nucmer.__file__)) data_dir = os.path.join(modules_dir, 'tests', 'data') class TestRunner(unittest.TestCase): def test_nucmer_command(self): '''test _nucmer_command''' tests = [ [nucmer.Runner('ref', 'qry', 'outfile'), 'nucmer -p pre ref qry'], [nucmer.Runner('ref', 'qry', 'outfile', breaklen=42), 'nucmer -p pre -b 42 ref qry'], [nucmer.Runner('ref', 'qry', 'outfile', diagdiff=11), 'nucmer -p pre -D 11 ref qry'], [nucmer.Runner('ref', 'qry', 'outfile', diagdiff=11, promer=True), 'promer -p pre ref qry'], [nucmer.Runner('ref', 'qry', 'outfile', maxmatch=True), 'nucmer -p pre --maxmatch ref qry'], [nucmer.Runner('ref', 'qry', 'outfile', simplify=False), 'nucmer -p pre --nosimplify ref qry'], [nucmer.Runner('ref', 'qry', 'outfile', promer=True), 'promer -p pre ref qry'], [nucmer.Runner('ref', 'qry', 'outfile', promer=True, breaklen=42), 'promer -p pre -b 42 ref qry'], [nucmer.Runner('ref', 'qry', 'outfile', promer=True, maxmatch=True), 'promer -p pre --maxmatch ref qry'], [nucmer.Runner('ref', 'qry', 'outfile', promer=True, simplify=False), 'promer -p pre ref qry'] ] for l in tests: self.assertEqual(l[0]._nucmer_command('ref', 'qry', 'pre'), l[1]) def test_delta_filter_command(self): '''test _delta_filter_command''' tests = [ [nucmer.Runner('ref', 'qry', 'outfile'), 'delta-filter infile > outfile'], [nucmer.Runner('ref', 'qry', 'outfile', min_id=42), 'delta-filter -i 42 infile > outfile'], [nucmer.Runner('ref', 'qry', 'outfile', min_length=43), 'delta-filter -l 43 infile > outfile'], ] for l in tests: self.assertEqual(l[0]._delta_filter_command('infile', 'outfile'), l[1]) def test_show_coords_command(self): '''test _show_coords_command''' tests = [ [nucmer.Runner('ref', 'qry', 'outfile', coords_header=False), 'show-coords -dTlro -H infile > outfile'], [nucmer.Runner('ref', 'qry', 'outfile'), 'show-coords -dTlro infile > outfile'] ] for l in tests: self.assertEqual(l[0]._show_coords_command('infile', 'outfile'), l[1]) def test_show_snps_command(self): '''test _show_snps_command''' tests = [ [nucmer.Runner('ref', 'qry', 'outfile', snps_header=False), 'show-snps -TClr -H infile > outfile'], [nucmer.Runner('ref', 'qry', 'outfile'), 'show-snps -TClr infile > outfile'] ] for l in tests: self.assertEqual(l[0]._show_snps_command('infile', 'outfile'), l[1]) def test_write_script_no_snps(self): '''test _write_script no snps''' tmp_script = 'tmp.script.sh' r = nucmer.Runner('ref', 'qry', 'outfile') r._write_script(tmp_script, 'ref', 'qry', 'outfile') expected = os.path.join(data_dir, 'nucmer_test_write_script_no_snps.sh') self.assertTrue(filecmp.cmp(expected, tmp_script, shallow=False)) os.unlink(tmp_script) def test_write_script_with_snps(self): '''test _write_script with snps''' tmp_script = 'tmp.script.sh' r = nucmer.Runner('ref', 'qry', 'outfile', show_snps='outfile.snps') r._write_script(tmp_script, 'ref', 'qry', 'outfile') expected = os.path.join(data_dir, 'nucmer_test_write_script_with_snps.sh') self.assertTrue(filecmp.cmp(expected, tmp_script, shallow=False)) os.unlink(tmp_script) def test_run_nucmer(self): '''test run_nucmer''' qry = os.path.join(data_dir, 'nucmer_test_qry.fa') ref = os.path.join(data_dir, 'nucmer_test_ref.fa') tmp_out = 'tmp.nucmer.out' runner = nucmer.Runner(ref, qry, tmp_out, coords_header=False, show_snps=True, snps_header=False) runner.run() expected = os.path.join(data_dir, 'nucmer_test_out.coords') self.assertTrue(filecmp.cmp(tmp_out, expected, shallow=False)) self.assertTrue(filecmp.cmp(tmp_out + '.snps', expected + '.snps', shallow=False)) os.unlink(tmp_out) os.unlink(tmp_out + '.snps') pymummer-0.7.0/pymummer/tests/snp_file_test.py000066400000000000000000000054061265635035100216310ustar00rootroot00000000000000import unittest import os from pymummer import snp_file, snp, variant modules_dir = os.path.dirname(os.path.abspath(snp_file.__file__)) data_dir = os.path.join(modules_dir, 'tests', 'data') class TestUtils(unittest.TestCase): def test_snp_file(self): '''test coords_file''' expected = [ '\t'.join(['133', 'G', '.', '122', '1', '122', '500', '489', '1', '1', 'ref', 'qry']), '\t'.join(['143', '.', 'C', '131', '1', '132', '500', '489', '1', '1', 'ref', 'qry']), '\t'.join(['253', 'T', 'A', '242', '120', '242', '500', '489', '1', '1', 'ref', 'qry']) ] expected = [snp.Snp(x) for x in expected] infiles = [os.path.join(data_dir, 'snp_file_test_with_header.snps'), os.path.join(data_dir, 'snp_file_test_no_header.snps')] for fname in infiles: fr = snp_file.reader(fname) snps = [x for x in fr] self.assertEqual(snps, expected) def test_get_all_variants(self): '''Test load all variants from file''' deletion_snps = [ '\t'.join(['125', 'T', '.', '124', '1', '124', '500', '497', '1', '1', 'ref1', 'qry1']), '\t'.join(['126', 'A', '.', '124', '1', '124', '500', '497', '1', '1', 'ref1', 'qry1']), '\t'.join(['127', 'C', '.', '124', '1', '124', '500', '497', '1', '1', 'ref1', 'qry1']), ] deletion_snps = [snp.Snp(x) for x in deletion_snps] deletion_variant = variant.Variant(deletion_snps[0]) deletion_variant.update_indel(deletion_snps[1]) deletion_variant.update_indel(deletion_snps[2]) just_a_snp = '\t'.join(['386', 'C', 'T', '383', '115', '115', '500', '497', '1', '1', 'ref1', 'qry1']) snp_variant = variant.Variant(snp.Snp(just_a_snp)) insertion_snps = [ '\t'.join(['479', '.', 'G', '480', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']), '\t'.join(['479', '.', 'A', '481', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']), '\t'.join(['479', '.', 'T', '482', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']), '\t'.join(['479', '.', 'A', '483', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']), ] insertion_snps = [snp.Snp(x) for x in insertion_snps] insertion_variant = variant.Variant(insertion_snps[0]) for i in range(1, len(insertion_snps)): insertion_variant.update_indel(insertion_snps[i]) variants_from_file = snp_file.get_all_variants(os.path.join(data_dir, 'snp_file_test_get_all_variants.snps')) self.assertEqual(len(variants_from_file), 3) self.assertEqual(variants_from_file[0], deletion_variant) self.assertEqual(variants_from_file[1], snp_variant) self.assertEqual(variants_from_file[2], insertion_variant) pymummer-0.7.0/pymummer/tests/snp_test.py000066400000000000000000000010311265635035100206200ustar00rootroot00000000000000import unittest import os from pymummer import snp modules_dir = os.path.dirname(os.path.abspath(snp.__file__)) data_dir = os.path.join(modules_dir, 'tests', 'data') class TestSnp(unittest.TestCase): def test_str(self): '''Test __str__''' l_in = ['187', 'A', 'C', '269', '187', '187', '654', '853', '1', '1', 'ref_name', 'qry_name'] # only use columns 0-3, 6-7, 10-11 l_out = l_in[:4] + l_in[6:8] + l_in[10:] s = snp.Snp('\t'.join(l_in)) self.assertEqual(str(s), '\t'.join(l_out)) pymummer-0.7.0/pymummer/tests/syscall_test.py000066400000000000000000000006061265635035100215010ustar00rootroot00000000000000import unittest import os from pymummer import syscall class TestSyscall(unittest.TestCase): def test_run_fail(self): '''Test that run raises error when command fails''' with self.assertRaises(syscall.Error): syscall.run('notacommandandthrowerror') def test_run_ok(self): '''Test run is ok on command that works''' syscall.run('ls') pymummer-0.7.0/pymummer/tests/variant_test.py000066400000000000000000000127541265635035100215020ustar00rootroot00000000000000import unittest import copy import os from pymummer import variant, snp modules_dir = os.path.dirname(os.path.abspath(variant.__file__)) data_dir = os.path.join(modules_dir, 'tests', 'data') class TestVariant(unittest.TestCase): def test_init(self): '''Test init gets correct variant type''' lines = [ ['42', 'T', 'A', '42', '42', '42', '1000', '1000', '1', '1', 'ref', 'ref'], ['242', 'G', '.', '241', '1', '241', '1000', '1000', '1', '1', 'ref', 'ref'], ['300', '.', 'G', '298', '0', '298', '1000', '1000', '1', '1', 'ref', 'ref'] ] variants = [variant.Variant(snp.Snp('\t'.join(x))) for x in lines] expected = [variant.SNP, variant.DEL, variant.INS] for i in range(len(lines)): self.assertEqual(variants[i].var_type, expected[i]) def test_update_indel_no_change(self): '''Test update_indel does nothing in the right cases''' initial_vars = [ snp.Snp('\t'.join(['42', 'A', 'C', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', 'A', 'C', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), ] to_add = [ snp.Snp('\t'.join(['142', 'A', '.', '1000', 'x', 'x', '2000', '3000', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['142', '.', 'A', '1000', 'x', 'x', '2000', '3000', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref2', 'qry'])), snp.Snp('\t'.join(['43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry2'])), snp.Snp('\t'.join(['44', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref2', 'qry'])), snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry2'])), snp.Snp('\t'.join(['44', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])), ] assert len(initial_vars) == len(to_add) for i in range(len(initial_vars)): var = variant.Variant(initial_vars[i]) var_original = copy.copy(var) self.assertFalse(var.update_indel(to_add[i])) self.assertEqual(var, var_original) def test_update_indel_insertion(self): '''Test update_indel extends insertions correctly''' insertion = variant.Variant(snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry']))) to_add = snp.Snp('\t'.join(['42', '.', 'C', '101', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])) expected = copy.copy(insertion) # coords stored zero-based, so subtract 1 from the real expected coords expected.ref_start = 41 expected.ref_end = 41 expected.ref_length = 300 expected.ref_name = 'ref' expected.ref_base = '.' expected.qry_start = 99 expected.qry_end = 100 expected.qry_length = 400 expected.qry_name = 'qry' expected.qry_base = 'AC' self.assertTrue(insertion.update_indel(to_add)) self.assertEqual(expected, insertion) def test_update_indel_deletion(self): '''Test update_indel extends deletions correctly''' deletion = variant.Variant(snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry']))) to_add = snp.Snp('\t'.join(['43', 'C', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref', 'qry'])) expected = copy.copy(deletion) # coords stored zero-based, so subtract 1 from the real expected coords expected.ref_start = 41 expected.ref_end = 42 expected.ref_length = 300 expected.ref_name = 'ref' expected.ref_base = 'AC' expected.qry_start = 99 expected.qry_end = 99 expected.qry_length = 400 expected.qry_name = 'qry' expected.qry_base = '.' self.assertTrue(deletion.update_indel(to_add)) self.assertEqual(expected, deletion) pymummer-0.7.0/pymummer/variant.py000066400000000000000000000051731265635035100172760ustar00rootroot00000000000000class Error (Exception): pass SNP = 1 DEL = 2 INS = 3 var_types = { 1: 'SNP', 2: 'DEL', 3: 'INS', } class Variant: def __init__(self, snp): '''Create a Variant object from a pymummer.snp.Snp object''' if snp.ref_base == '.': self.var_type = INS self.qry_base = snp.qry_base self.ref_base = '.' elif snp.qry_base == '.': self.var_type = DEL self.qry_base = '.' self.ref_base = snp.ref_base elif '.' not in [snp.ref_base, snp.qry_base]: self.var_type = SNP self.ref_base = snp.ref_base self.qry_base = snp.qry_base else: raise Error('Error constructing Variant from pymummer.snp.Snp:' + str(snp)) self.ref_start = snp.ref_pos self.ref_end = snp.ref_pos self.ref_length = snp.ref_length self.ref_name = snp.ref_name self.qry_start = snp.qry_pos self.qry_end = snp.qry_pos self.qry_length = snp.qry_length self.qry_name = snp.qry_name def __eq__(self, other): return type(other) is type(self) and self.__dict__ == other.__dict__ def __str__(self): return '\t'.join([ str(self.ref_start + 1), str(self.ref_end + 1), str(self.ref_length), str(self.ref_name), self.ref_base, str(self.qry_start + 1), str(self.qry_end + 1), str(self.qry_length), str(self.qry_name), self.qry_base ]) def update_indel(self, nucmer_snp): '''Indels are reported over multiple lines, 1 base insertion or deletion per line. This method extends the current variant by 1 base if it's an indel and adjacent to the new SNP and returns True. If the current variant is a SNP, does nothing and returns False''' new_variant = Variant(nucmer_snp) if self.var_type not in [INS, DEL] \ or self.var_type != new_variant.var_type \ or self.qry_name != new_variant.qry_name \ or self.ref_name != new_variant.ref_name: return False if self.var_type == INS \ and self.ref_start == new_variant.ref_start \ and self.qry_end + 1 == new_variant.qry_start: self.qry_base += new_variant.qry_base self.qry_end += 1 return True if self.var_type == DEL \ and self.qry_start == new_variant.qry_start \ and self.ref_end + 1 == new_variant.ref_start: self.ref_base += new_variant.ref_base self.ref_end += 1 return True return False pymummer-0.7.0/setup.py000066400000000000000000000023431265635035100151130ustar00rootroot00000000000000import os import glob import shutil import sys from setuptools import setup, find_packages required_progs = ['nucmer', 'show-coords', 'show-snps', 'delta-filter'] found_all_progs = True print('Checking MUMmer programs found in path:') for program in required_progs: if shutil.which(program) is None: found_all_progs = False found = ' NOT FOUND' else: found = ' OK' print(found, program, sep='\t') if not found_all_progs: print('Cannot install because some programs from the MUMer package not found.', file=sys.stderr) sys.exit(1) setup( name='pymummer', version='0.7.0', description='Wrapper for MUMmer', packages = find_packages(), author='Martin Hunt, Nishadi De Silva', author_email='path-help@sanger.ac.uk', url='https://github.com/sanger-pathogens/pymummer', test_suite='nose.collector', install_requires=['pyfastaq >= 3.10.0'], tests_require=['nose >= 1.3'], license='GPLv3', classifiers=[ 'Development Status :: 4 - Beta', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 3 :: Only', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', ], )