debian/changelog

+seqmagick (0.7.0-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+  TODO: https://github.com/fhcrc/seqmagick/issues/73
+
+ -- Andreas Tille <tille@debian.org>  Thu, 22 Jun 2017 12:03:20 +0200

debian/compat

+11

debian/control

+Source: seqmagick
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~),
+               dh-python,
+               python3-all,
+               python3-setuptools,
+               python3-nose,
+               python3-biopython
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/seqmagick
+Vcs-Git: https://salsa.debian.org/med-team/seqmagick.git
+Homepage: https://github.com/fhcrc/seqmagick/
+
+Package: seqmagick
+Architecture: all
+Depends: ${python3:Depends},
+         ${misc:Depends},
+         python3-biopython
+Description: imagemagick-like frontend to Biopython SeqIO
+ Seqmagick is a little utility to expose the file format conversion
+ in BioPython in a convenient way.
+ .
+ Features include:
+ .
+  * Modifying sequences:
+    - Remove gaps
+    - Reverse & reverse complement
+    - Trim to a range of residues
+    - Change case
+    - Sort by length or ID
+  * Displaying information about sequence files
+  * Subsetting sequence files by:
+    - Position
+    - ID
+    - Deduplication
+  * Filtering sequences by quality score
+  * Trimming alignments to a region of interest defined by the forward
+    and reverse primers

debian/copyright

+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: https://github.com/fhcrc/seqmagick/releases
+
+Files: *
+Copyright: 2014-2017 Matsen Group
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille@debian.org>
+License: GPL-3+
+
+License: GPL-3+
+    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 3 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.
+ .
+ On Debian systems you can find a copy of the full text of the GNU General
+ Public License version 3 at /usr/share/common-licenses/GPL-3.

debian/createmanpages

+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=seqmagick
+help2man --no-info --no-discard-stderr  \
+         --name='Manipulate sequence files' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+

debian/manpages

+debian/*.1

debian/rules

+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+%:
+	dh $@ --with python3 --buildsystem=pybuild

debian/seqmagick.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH SEQMAGICK "1" "June 2017" "seqmagick 0.6.1" "User Commands"
+.SH NAME
+seqmagick \- Manipulate sequence files
+.SH SYNOPSIS
+usage: seqmagick [\-h] [\-V] [\-v] [\-q]
+.IP
+{help,convert,info,mogrify,primer\-trim,quality\-filter,extract\-ids,backtrans\-align}
+\&...
+.SH DESCIPTION
+Seqmagick is a little utility to expose the file format conversion
+in BioPython in a convenient way.
+.SH OPTIONS
+.SS "positional arguments:"
+.IP
+{help,convert,info,mogrify,primer\-trim,quality\-filter,extract\-ids,backtrans\-align}
+.TP
+help
+Detailed help for actions using help <action>
+.TP
+convert
+Convert between sequence formats
+.TP
+info
+Info action
+.TP
+mogrify
+Modify sequence file(s) in place.
+.TP
+primer\-trim
+Find a primer sequence in a gapped alignment, trim to
+amplicon
+.TP
+quality\-filter
+Filter reads based on quality scores
+.TP
+extract\-ids
+Extract the sequence IDs from a file
+.TP
+backtrans\-align
+Given a protein alignment and unaligned nucleotides,
+align the nucleotides using the protein alignment.
+Protein and nucleotide sequence files must contain the
+same number of sequences, in the same order, with the
+same IDs.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Print the version number and exit
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Be more verbose. Specify \fB\-vv\fR or \fB\-vvv\fR for even more
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Suppress output
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/source/format

+3.0 (quilt)

debian/watch

+version=4
+
+https://github.com/fhcrc/seqmagick/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)