[med-svn] [python-biotools] 01/02: Add manpages

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository python-biotools.

commit 94e3867d5e22db1592f2463ba1370361dfca9972
Author: Andreas Tille <tille at debian.org>
Date:   Thu Mar 2 20:06:26 2017 +0100

    Add manpages
---
 debian/createmanpages            | 28 +++++++++++++++++
 debian/grepseq.1                 | 43 +++++++++++++++++++++++++
 debian/prok-geneseek.1           | 68 ++++++++++++++++++++++++++++++++++++++++
 debian/python3-biotools.manpages |  1 +
 4 files changed, 140 insertions(+)

diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..e197ec8
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,28 @@
+#!/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 $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=prok-geneseek
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='Seek genes in prokaryotes' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=grepseq
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='Seek pattern in 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
+
diff --git a/debian/grepseq.1 b/debian/grepseq.1
new file mode 100644
index 0000000..04183a0
--- /dev/null
+++ b/debian/grepseq.1
@@ -0,0 +1,43 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH GREPSEQ "1" "March 2017" "grepseq 1.2.12" "User Commands"
+.SH NAME
+grepseq \- <optional description of the program>
+.SH SYNOPSIS
+.B grepseq
+[\fI\,options\/\fR] \fI\,<pattern> <files \/\fR...\fI\,>\/\fR
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-c\fR, \fB\-\-count\fR
+Suppress normal output; instead print a count of
+matching lines for each input file. With the \fB\-v\fR,
+\fB\-\-invert\-match\fR option (see below), count non\-matching
+lines.
+.TP
+\fB\-H\fR, \fB\-\-with\-filename\fR
+Print the filename for each match.
+.TP
+\fB\-i\fR, \fB\-\-ignore\-case\fR
+Ignore case distinctions in both the pattern and
+input files.
+.TP
+\fB\-m\fR NUM, \fB\-\-max\-count\fR=\fI\,NUM\/\fR
+Stop reading a file after NUM matching lines. When
+the \fB\-c\fR or \fB\-\-count\fR option is also used, grepseq does
+not output a count greater than NUM. When the \fB\-v\fR or
+\fB\-\-invert\-match\fR option is also used, grep stops after
+outputting NUM non\-matching lines.
+.TP
+\fB\-N\fR, \fB\-\-names\-only\fR
+Search only sequence names. Cannot be used with \fB\-S\fR.
+.TP
+\fB\-S\fR, \fB\-\-sequences\-only\fR
+Search only sequences. Cannot be used with \fB\-N\fR.
+.TP
+\fB\-v\fR, \fB\-\-invert\-match\fR
+Invert the sense of matching, to select non\-matching
+lines.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/prok-geneseek.1 b/debian/prok-geneseek.1
new file mode 100644
index 0000000..3329ec3
--- /dev/null
+++ b/debian/prok-geneseek.1
@@ -0,0 +1,68 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH PROK-GENESEEK "1" "March 2017" "prok-geneseek 1.2.12" "User Commands"
+.SH NAME
+prok-geneseek \- <optional description of the program>
+.SH SYNOPSIS
+.B prok-geneseek
+[\fI\,options\/\fR] \fI\,<database> <sequences \/\fR...\fI\,>\/\fR
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-S\fR START, \fB\-\-start\fR=\fI\,START\/\fR
+define a start codon [default: \fB\-S\fR ATG]
+.TP
+\fB\-E\fR STOP, \fB\-\-stop\fR=\fI\,STOP\/\fR
+define a stop codon [default: \fB\-E\fR TAG \fB\-E\fR TAA \fB\-E\fR TGA]
+.TP
+\fB\-j\fR THREADS, \fB\-\-threads\fR=\fI\,THREADS\/\fR
+number of threads [default: 16]
+.TP
+\fB\-p\fR PROCESSES, \fB\-\-processes\fR=\fI\,PROCESSES\/\fR
+number of parallel processes to run [default: 2]
+.TP
+\fB\-e\fR EVALUE, \fB\-\-evalue\fR=\fI\,EVALUE\/\fR
+maximum e\-value [default: 1e\-30]
+.TP
+\fB\-I\fR IDENTITY, \fB\-\-identity\fR=\fI\,IDENTITY\/\fR
+minimum percent identity [default: 0.45]
+.TP
+\fB\-L\fR FRACTION, \fB\-\-length\fR=\fI\,FRACTION\/\fR
+allowable relative error in hit length [default: 0.2]
+.TP
+\fB\-O\fR bases, \fB\-\-orflen\fR=\fI\,bases\/\fR
+minimum allowable length for ORFs [default: 300]
+.TP
+\fB\-d\fR DIRECTORY, \fB\-\-directory\fR=\fI\,DIRECTORY\/\fR
+set working directory [default: current]
+.TP
+\fB\-P\fR PLOTTER, \fB\-\-plotter\fR=\fI\,PLOTTER\/\fR
+plotting module [default: biotools.analysis.plot]
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+print debug messages [default: False]
+.TP
+\fB\-\-no\-plots\fR
+suppress the drawing of plots [default: False]
+.TP
+\fB\-\-no\-predict\fR
+don't predict genes, instead treat the input files as
+predicted genes [default: False]
+.TP
+\fB\-\-no\-cluster\fR
+don't cluster the sequences, instead treat the input
+files as alignments [default: False]
+.TP
+\fB\-\-no\-rename\fR
+don't rename the fasta and clustal files [default:
+False]
+.TP
+\fB\-\-no\-reports\fR
+don't generate files for variance data [default:
+False]
+.TP
+\fB\-\-no\-calculation\fR
+don't calculate sequence variance [default: False]
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/python3-biotools.manpages b/debian/python3-biotools.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/python3-biotools.manpages
@@ -0,0 +1 @@
+debian/*.1

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