[med-svn] [ecopcr] 02/02: Try to automatically generate manpages
Andreas Tille
tille at debian.org
Wed Jun 24 19:21:19 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ecopcr.
commit b495b92f678eb317f694100a9ebbee4cef2b1814
Author: Andreas Tille <tille at debian.org>
Date: Wed Jun 24 21:14:42 2015 +0200
Try to automatically generate manpages
---
debian/control | 3 +-
debian/createmanpages | 26 +++++++++++++
debian/install | 7 ++--
debian/man/ecoPCR.1 | 96 +++++++++++++++++++++++++++++++++++++++++++++++
debian/man/ecoPCRFormat.1 | 22 +++++++++++
debian/man/ecofind.1 | 49 ++++++++++++++++++++++++
debian/man/ecogrep.1 | 52 +++++++++++++++++++++++++
debian/manpages | 1 +
8 files changed, 252 insertions(+), 4 deletions(-)
diff --git a/debian/control b/debian/control
index d40a7fd..fa6edab 100644
--- a/debian/control
+++ b/debian/control
@@ -16,7 +16,8 @@ Package: ecopcr
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- ${python3:Depends}
+ ${python3:Depends},
+ python3-reportlab
Description: estimate PCR barcode primers quality
DNA barcoding is a tool for characterizing the species origin using a
short sequence from a standard position and agreed upon position in the
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..d0ab362
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,26 @@
+#!/bin/sh
+MANDIR=debian/man
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='searching for sequence and taxonomy hybriding with given primers' \
+ --version-string="$VERSION" ecoPCR > $MANDIR/ecoPCR.1
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='searching for taxonomic and rank and taxonomy id for given regular expression patterns' \
+ --version-string="$VERSION" ecofind > $MANDIR/ecofind.1
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='filtering ecoPCR result based on taxonomic id filter and regular expression pattern' \
+ --version-string="$VERSION" ecogrep > $MANDIR/ecogrep.1
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='tool belonging to ecoPCR package' \
+ --version-string="$VERSION" ecoPCRFormat > $MANDIR/ecoPCRFormat.1
+sed -i 's/ecoPCRFormat\.py/ecoPCRFormat/g' $MANDIR/ecoPCRFormat.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/install b/debian/install
index e28f56b..68fee8b 100644
--- a/debian/install
+++ b/debian/install
@@ -1,3 +1,4 @@
-src/ecoPCR usr/bin
-src/ecofind usr/bin
-src/ecogrep usr/bin
+src/ecoPCR usr/bin
+src/ecofind usr/bin
+src/ecogrep usr/bin
+src/ecoisundertaxon usr/bin
diff --git a/debian/man/ecoPCR.1 b/debian/man/ecoPCR.1
new file mode 100644
index 0000000..26ddaef
--- /dev/null
+++ b/debian/man/ecoPCR.1
@@ -0,0 +1,96 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH ECOPCR "1" "June 2015" "ecoPCR 0.5.0" "User Commands"
+.SH NAME
+ecoPCR \- searching for sequence and taxonomy hybriding with given primers
+.SH DESCRIPTION
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+ecoPCR Version 0.2
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+synopsis : searching for sequence and taxonomy hybriding with given primers
+usage: ecoPCR [options] <nucleotidic patterns>
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+options:
+\fB\-a\fR : Salt concentration in M for Tm computation (default 0.05 M)
+.PP
+\fB\-c\fR : Consider that the database sequences are [c]ircular
+.PP
+\fB\-d\fR : [D]atabase : to match the expected format, the database
+.IP
+has to be formated first by the ecoPCRFormat.py program located.
+in the tools directory.
+ecoPCRFormat.py creates three file types :
+.IP
+\&.sdx : contains the sequences
+\&.tdx : contains information concerning the taxonomy
+\&.rdx : contains the taxonomy rank
+.IP
+ecoPCR needs all the file type. As a result, you have to write the
+database radical without any extension. For example \fI\,/ecoPCRDB/gbmam\/\fP
+.PP
+\fB\-D\fR : Keeps the specified number of nucleotides on each side of the in silico
+.IP
+amplified sequences (including the amplified DNA fragment plus the two target
+sequences of the primers).
+.PP
+\fB\-e\fR : [E]rror : max errors allowed by oligonucleotide (0 by default)
+.PP
+\fB\-h\fR : [H]elp \- print <this> help
+.PP
+\fB\-i\fR : [I]gnore the given taxonomy id.
+.IP
+Taxonomy id are available using the ecofind program.
+see its help typing ecofind \fB\-h\fR for more information.
+.PP
+\fB\-k\fR : [K]ingdom mode : set the kingdom mode
+.IP
+super kingdom mode by default.
+.PP
+\fB\-l\fR : minimum [L]ength : define the minimum amplication length.
+.PP
+\fB\-L\fR : maximum [L]ength : define the maximum amplicationlength.
+.PP
+\fB\-m\fR : Salt correction method for Tm computation (SANTALUCIA : 1
+.IP
+or OWCZARZY:2, default=1)
+.PP
+\fB\-r\fR : [R]estricts the search to the given taxonomic id.
+.IP
+Taxonomy id are available using the ecofind program.
+see its help typing ecofind \fB\-h\fR for more information.
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+first argument : oligonucleotide for direct strand
+.PP
+second argument : oligonucleotide for reverse strand
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+Table result description :
+column 1 : accession number
+column 2 : sequence length
+column 3 : taxonomic id
+column 4 : rank
+column 5 : species taxonomic id
+column 6 : scientific name
+column 7 : genus taxonomic id
+column 8 : genus name
+column 9 : family taxonomic id
+column 10 : family name
+column 11 : super kingdom taxonomic id
+column 12 : super kingdom name
+column 13 : strand (direct or reverse)
+column 14 : first oligonucleotide
+column 15 : number of errors for the first strand
+column 16 : Tm for hybridization of primer 1 at this site
+column 17 : second oligonucleotide
+column 18 : number of errors for the second strand
+column 19 : Tm for hybridization of primer 1 at this site
+column 20 : amplification length
+column 21 : sequence
+column 22 : definition
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+http://www.grenoble.prabi.fr/trac/ecoPCR/
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
diff --git a/debian/man/ecoPCRFormat.1 b/debian/man/ecoPCRFormat.1
new file mode 100644
index 0000000..9de9021
--- /dev/null
+++ b/debian/man/ecoPCRFormat.1
@@ -0,0 +1,22 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH ECOPCRFORMAT "1" "June 2015" "ecoPCRFormat 0.5.0" "User Commands"
+.SH NAME
+ecoPCRFormat \- tool belonging to ecoPCR package
+.SH DESCRIPTION
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+ecoPCRFormat
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+ecoPCRFormat [option] <argument>
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+\fB\-e\fR \fB\-\-embl\fR :[E]mbl format
+\fB\-f\fR \fB\-\-fasta\fR :[F]asta format
+\fB\-g\fR \fB\-\-genbank\fR :[G]enbank format
+\fB\-h\fR \fB\-\-help\fR :[H]elp \- print this help
+\fB\-n\fR \fB\-\-name\fR :[N]ame of the new database created
+\fB\-t\fR \fB\-\-taxonomy\fR :[T]axonomy \- path to the taxonomy database
+.IP
+:bcp\-like dump from GenBank taxonomy database.
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
diff --git a/debian/man/ecofind.1 b/debian/man/ecofind.1
new file mode 100644
index 0000000..a2b8bb2
--- /dev/null
+++ b/debian/man/ecofind.1
@@ -0,0 +1,49 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH ECOFIND "1" "June 2015" "ecofind 0.5.0" "User Commands"
+.SH NAME
+ecofind \- searching for taxonomic and rank and taxonomy id for given regular expression patterns
+.SH DESCRIPTION
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+ecofind Version 0.1
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+synopsis : searching for taxonomic and rank and
+.TP
+taxonomy id for given regular
+expression patterns
+.PP
+usage: ecofind [options] <patterns>
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+options:
+\fB\-a\fR : [A]ll enable the search on all alternative names and not only scientific names.
+.PP
+\fB\-d\fR : [D]atabase containing the taxonomy.
+.IP
+To match the expected format, the database
+has to be formated first by the ecoPCRFormat.py
+program located in the tools directory.
+Write the database radical without any extension.
+.PP
+\fB\-h\fR : [H]elp \- print <this> help
+.PP
+\fB\-l\fR : [L]ist all taxonomic rank available for \fB\-r\fR option
+.PP
+\fB\-P\fR : [P]ath : add a column containing the full path for each displayed taxon
+.PP
+\fB\-p\fR : [P]arents : specifiying this option displays all parental tree's information for the given taxid.
+.PP
+\fB\-r\fR : [R]estrict to given taxonomic rank
+.PP
+\fB\-s\fR : [S]ons: specifiying this option displays all subtree's information for the given taxid.
+.PP
+\fB\-P\fR : Display taxonomic [P]ath as suplementary column in output
+.PP
+arguments:
+<taxon> name pattern bearing regular expressions
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+http://www.grenoble.prabi.fr/trac/ecoPCR/
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
diff --git a/debian/man/ecogrep.1 b/debian/man/ecogrep.1
new file mode 100644
index 0000000..e97656d
--- /dev/null
+++ b/debian/man/ecogrep.1
@@ -0,0 +1,52 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1.
+.TH ECOGREP "1" "June 2015" "ecogrep 0.5.0" "User Commands"
+.SH NAME
+ecogrep \- filtering ecoPCR result based on taxonomic id filter and regular expression pattern
+.SH DESCRIPTION
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+ecogrep Version 0.1
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+synopsis : filtering ecoPCR result based on
+taxonomic id filter and regular expression pattern
+usage: ecogrep [options] filename
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+options:
+\fB\-1\fR : [FIRST] : compare the given pattern with direct strand oligonucleotide
+.TP
+\fB\-2\fR
+: [SECOND] : compare the given pattern with reverse strand oligonucleotide
+.TP
+\fB\-d\fR
+: [D]atabase containing taxonomic information
+.TP
+\fB\-e\fR
+: [E]rrors : max error allowed in pattern match (option\-1, \fB\-2\fR and \fB\-p\fR) (0 by default)
+.TP
+\fB\-p\fR
+: [P]attern : oligonucleotide pattern
+.TP
+\fB\-h\fR
+: [H]elp : print <this> help
+.TP
+\fB\-i\fR
+: [I]gnore subtree under given taxonomic id
+.TP
+\fB\-r\fR
+: [R]estrict search to subtree under given taxomic id
+.TP
+\fB\-v\fR
+: in[V]ert the sense of matching, to select non\-matching lines.
+.IP
+argument:
+ecoPCR ouput file name
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+.IP
+http://www.grenoble.prabi.fr/trac/ecoPCR/
+.PP
+\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..13cdaf4
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/man/*.1
--
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