debian/0000755000000000000000000000000012157614062007172 5ustar debian/control0000644000000000000000000000313712157577355010616 0ustar Source: python-pynast Section: python Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Tim Booth Build-Depends: debhelper (>= 9), python (>= 2.6.6-3~), python-cogent (>= 1.5.3), python-sphinx Standards-Version: 3.9.4 Homepage: http://pynast.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-pynast/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/python-pynast/trunk/ X-Python-Version: >= 2.5 Package: pynast Architecture: all Depends: ${misc:Depends}, ${python:Depends}, libjs-jquery, libjs-underscore Provides: python-pynast Replaces: python-pynast Conflicts: python-pynast Description: alignment of short DNA sequences The package provices a reimplementation of the Nearest Alignment Space Termination tool in Python. It was prepared for next generation sequencers. . Given a set of sequences and a template alignment, PyNAST will align the input sequences against the template alignment, and return a multiple sequence alignment which contains the same number of positions (or columns) as the template alignment. This facilitates the analysis of new sequences in the context of existing alignments, and additional data derived from existing alignments such as phylogenetic trees. Because any protein or nucleic acid sequences and template alignments can be provided, PyNAST is not limited to the analysis of 16s rDNA sequences. debian/pynast.10000644000000000000000000000362511665135242010601 0ustar .TH VERSION: "1" "August 2011" "Version: pynast 1.1" "User Commands" .SH NAME PyNAST \- alignment of short DNA sequences .SH SYNOPSIS .B pynast [\fIoptions\fR] \fI{\-i input_fp \-t template_fp}\fR .SH DESCRIPTION [] indicates optional input (order unimportant) {} indicates required input (order unimportant) .SS "Example usage:" .IP pynast \fB\-i\fR my_input.fasta \fB\-t\fR my_template.fasta .SH OPTIONS .TP \fB\-\-version\fR show program's version number and exit .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit .TP \fB\-t\fR TEMPLATE_FP, \fB\-\-template_fp\fR=\fITEMPLATE_FP\fR path to template alignment file [REQUIRED] .TP \fB\-i\fR INPUT_FP, \fB\-\-input_fp\fR=\fIINPUT_FP\fR path to input fasta file [REQUIRED] .TP \fB\-v\fR, \fB\-\-verbose\fR Print status and other information during execution [default: False] .TP \fB\-p\fR MIN_PCT_ID, \fB\-\-min_pct_id\fR=\fIMIN_PCT_ID\fR minimum percent sequence identity to consider a sequence a match [default: 75.0] .TP \fB\-l\fR MIN_LEN, \fB\-\-min_len\fR=\fIMIN_LEN\fR minimum sequence length to include in NAST alignment [default: 1000] .TP \fB\-m\fR PAIRWISE_ALIGNMENT_METHOD, \fB\-\-pairwise_alignment_method\fR=\fIPAIRWISE_ALIGNMENT_METHOD\fR method for performing pairwise alignment [default: uclust] .TP \fB\-a\fR FASTA_OUT_FP, \fB\-\-fasta_out_fp\fR=\fIFASTA_OUT_FP\fR path to store resulting alignment file [default: derived from input filepath] .TP \fB\-g\fR LOG_FP, \fB\-\-log_fp\fR=\fILOG_FP\fR path to store log file [default: derived from input filepath] .TP \fB\-f\fR FAILURE_FP, \fB\-\-failure_fp\fR=\fIFAILURE_FP\fR path to store file of seqs which fail to align [default: derived from input filepath] .TP \fB\-e\fR MAX_E_VALUE, \fB\-\-max_e_value\fR=\fIMAX_E_VALUE\fR Depreciated. Will be removed in PyNAST 1.2 .TP \fB\-d\fR BLAST_DB, \fB\-\-blast_db\fR=\fIBLAST_DB\fR Depreciated. Will be removed in PyNAST 1.2 .SH "SEE ALSO" http://pynast.sourceforge.net debian/links0000644000000000000000000000026111665135631010237 0ustar usr/share/javascript/jquery/jquery.js usr/share/doc/pynast/html/_static/jquery.js usr/share/javascript/underscore/underscore.js usr/share/doc/pynast/html/_static/underscore.js debian/rules0000755000000000000000000000101211665133674010254 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 #Allowing this to be overridden by environemnt helps with backports DEB_PYTHON_SUPPORT?=python2 %: dh $@ --with $(DEB_PYTHON_SUPPORT) override_dh_auto_build: dh_auto_build $(MAKE) -C doc html override_dh_auto_clean: dh_auto_clean $(MAKE) -C doc clean #Fix Lintian warning about jquery.js override_dh_installdocs: dh_installdocs -X.buildinfo #Don't compress .js files override_dh_compress: dh_compress -X.js debian/manpages0000644000000000000000000000002011626631053010677 0ustar debian/pynast.1 debian/watch0000644000000000000000000000011712157577355010237 0ustar version=3 http://qiime.org/pynast/ .*/PyNAST-([.0-9]+)\.(?:tgz|tar.gz|tar.bz2) debian/upstream0000644000000000000000000000073311752237613010763 0ustar Name: PyNAST Homepage: http://pynast.sourceforge.net/ Reference: Author: J. Gregory Caporaso and Kyle Bittinger and Frederic D. Bushman and Todd Z. DeSantis and Gary L. Andersen and Rob Knight Title: > PyNAST: a flexible tool for aligning sequences to a template alignment Journal: Bioinformatics Volume: 26 Pages: 266-267. Year: 2010 DOI: 10.1093/bioinformatics/btp636 PMID: 19914921 URL: http://bioinformatics.oxfordjournals.org/content/26/2/266.long debian/copyright0000644000000000000000000000266111665131766011142 0ustar Format: http://dep.debian.net/deps/dep5/ Upstream-Name: PyNAST Upstream-Contact: Greg Caporaso , Rob Knight Source: http://pynast.sorceforge.net Files: * Copyright: © 2010, The PyNAST Project Greg Caporaso Kyle Bittinger Rob Knight License: GPL-2 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. Files: debian/* Copyright: © 2010 Sri Girish Srinivasa Murthy , © 2011 Steffen Moeller , Tim Booth , Andreas Tille License: GPL-2 Same as the software itself. debian/source/0000755000000000000000000000000012146352504010470 5ustar debian/source/format0000644000000000000000000000001411412043500011662 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000120111671476713011236 0ustar PyNAST for Debian ================= Since version 1.1, PyNAST no longer exactly matches the output of the origianl NAST program. Instead it focuses on getting better alignments. Users who wish to exactly match the results of NAST should download PyNAST 1.0. The package is named 'pynast', not 'nast', since that is the name of the python module. A man page for /usr/bin/pynast is still missing. The package was build as a dependency to qiime, so some external help as a contribtion to upstream and this Debian package by a rudimentary man page would be appreciated. -- Andreas Tille Tue, 29 Nov 2011 11:22:19 +0100 debian/changelog0000644000000000000000000000614312157603271011050 0ustar python-pynast (1.2-1) unstable; urgency=low * Upload to Debian -- Andreas Tille Mon, 17 Jun 2013 14:52:50 +0200 python-pynast (1.2-0biolinux1) precise; urgency=low * New upstream * New upstream location - changed watchfile -- Tim Booth Tue, 11 Jun 2013 15:37:30 +0100 python-pynast (1.1-4) unstable; urgency=low [ Charles Plessy ] * Renamed debian/upstream-metadata.yaml to debian/upstream. * Corrected VCS URLs (debian/control). [ Andreas Tille ] * debian/upstream: - Moved DOI/PMID to References section - Valid BibTeX authors field * debian/control: - Section: optional - Standards-Version: 3.9.4 (no changes needed) - Debhelper 9 (also in compat) - removed XS-Autobuild because package is in main - Drop Build-Depends: python-central Closes: #708889 -- Andreas Tille Mon, 20 May 2013 10:29:27 +0200 python-pynast (1.1-3) unstable; urgency=low [ Steffen Moeller ] * Rendering Tim's fixes available for Debian * Moving pynast from contrib to main. The dependency cogent got its non-freeness resolved. * Changing name from python-pynast to pynast. [ Andreas Tille ] * debian/control: - Added myself and Tim Booth to Uploaders - Fixed Vcs fields - Removed duplicated ${misc:Depends} - Removed unneeded ${shlibs:Depends} - Depends: libjs-jquery, libjs-underscore - Moved citation information from long description to upstream-metadata.yaml - Moved information about previous versions from long description to README.Debian - Provides/Replaces/Conflicts: python-pynast to enable smooth upgrades after renaming the package * debian/copyright: DEP5 * Dephelper 8 (control+compat) * debian/links: Link packages JavaScript libraries * debian/rules: remove incomplete links to JavaScript libraries * debian/doc-base: created docbase file * debian/pynast.1: escape hyphen character * debian/upstream-metadata.yaml: Citation information * debian/README.Debian: Replaced outdated and useless content by some information about previous upstream versions (previosely mentioned in long description) -- Andreas Tille Tue, 29 Nov 2011 11:22:19 +0100 python-pynast (1.1-2ubuntu4) lucid; urgency=low * Fix Lintian warning on docs, clean up build file * Allow building with either python2 or python-central * Renamed main package to pynast -- Tim Booth Fri, 26 Aug 2011 11:29:17 +0100 python-pynast (1.1-2ubuntu3) lucid; urgency=low * Rebuild for Lucid, lowered dependencies -- Tim Booth Fri, 26 Aug 2011 10:05:42 +0100 python-pynast (1.1-2) unstable; urgency=low * Transition to dh7 and dh_python2 * Adjusted uploaders, first upload to unstable * Documentation built with sphinx * Added man page -- Steffen Moeller Thu, 25 Aug 2011 23:19:06 +0200 python-pynast (1.1-1) experimental; urgency=low * Initial release (Closes: #587189) -- Sri Girish Srinivasa Murthy Sun, 25 Jul 2010 22:21:11 +0200 debian/doc-base0000644000000000000000000000150711665135646010606 0ustar Document: python-pynast Title: Python Nearest Alignment Space Termination tool Author: The PyNAST Project Abstract: alignment of short DNA sequences Given a set of sequences and a template alignment, PyNAST will align the input sequences against the template alignment, and return a multiple sequence alignment which contains the same number of positions (or columns) as the template alignment. This facilitates the analysis of new sequences in the context of existing alignments, and additional data derived from existing alignments such as phylogenetic trees. Because any protein or nucleic acid sequences and template alignments can be provided, PyNAST is not limited to the analysis of 16s rDNA sequences. Section: Science/Biology Format: html Files: /usr/share/doc/pynast/html/* Index: /usr/share/doc/pynast/html/index.html debian/compat0000644000000000000000000000000212146350711010364 0ustar 9 debian/docs0000644000000000000000000000003212157577355010055 0ustar README.md doc/_build/html