[med-svn] r22071 - in trunk/packages/srst2/trunk/debian: . mans patches
Andreas Tille
tille at moszumanska.debian.org
Wed Jun 1 22:19:25 UTC 2016
Author: tille
Date: 2016-06-01 22:19:24 +0000 (Wed, 01 Jun 2016)
New Revision: 22071
Added:
trunk/packages/srst2/trunk/debian/clean
trunk/packages/srst2/trunk/debian/doc-base
trunk/packages/srst2/trunk/debian/install
trunk/packages/srst2/trunk/debian/mans/VFDB_cdhit_to_csv.1
trunk/packages/srst2/trunk/debian/mans/VFDBgenus.1
trunk/packages/srst2/trunk/debian/mans/csv_to_gene_db.1
trunk/packages/srst2/trunk/debian/mans/get_all_vfdb.1
trunk/packages/srst2/trunk/debian/mans/get_genus_vfdb.1
trunk/packages/srst2/trunk/debian/patches/
trunk/packages/srst2/trunk/debian/patches/add_usr_bin_python_to_scripts.patch
trunk/packages/srst2/trunk/debian/patches/check_command_line_arguments.patch
trunk/packages/srst2/trunk/debian/patches/series
Modified:
trunk/packages/srst2/trunk/debian/control
trunk/packages/srst2/trunk/debian/rules
Log:
Manpages, doc-base
Added: trunk/packages/srst2/trunk/debian/clean
===================================================================
--- trunk/packages/srst2/trunk/debian/clean (rev 0)
+++ trunk/packages/srst2/trunk/debian/clean 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1 @@
+README*.html
Modified: trunk/packages/srst2/trunk/debian/control
===================================================================
--- trunk/packages/srst2/trunk/debian/control 2016-06-01 21:51:40 UTC (rev 22070)
+++ trunk/packages/srst2/trunk/debian/control 2016-06-01 22:19:24 UTC (rev 22071)
@@ -7,7 +7,8 @@
dh-python,
python-all,
python-setuptools,
- python-markdown
+ python-markdown,
+ dos2unix
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/srst2/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/srst2/trunk/
Added: trunk/packages/srst2/trunk/debian/doc-base
===================================================================
--- trunk/packages/srst2/trunk/debian/doc-base (rev 0)
+++ trunk/packages/srst2/trunk/debian/doc-base 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,13 @@
+Document: srst2
+Title: Short Read Sequence Typing for Bacterial Pathogens
+Author: Michael Inouye, Harriet Dashnow, Bernie Pope, Kathryn Holt
+Abstract: Short Read Sequence Typing for Bacterial Pathogens
+ This program is designed to take Illumina sequence data, a MLST database
+ and/or a database of gene sequences (e.g. resistance genes, virulence
+ genes, etc) and report the presence of STs and/or reference genes.
+Section: Science/Biology
+
+Format: html
+Index: /usr/share/doc/srst2/README.html
+Files: /usr/share/doc/srst2/*.html
+
Added: trunk/packages/srst2/trunk/debian/install
===================================================================
--- trunk/packages/srst2/trunk/debian/install (rev 0)
+++ trunk/packages/srst2/trunk/debian/install 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,2 @@
+database_clustering/*.py usr/share/srst2/database_clustering
+database_clustering/*.sh usr/share/srst2/database_clustering
Added: trunk/packages/srst2/trunk/debian/mans/VFDB_cdhit_to_csv.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/VFDB_cdhit_to_csv.1 (rev 0)
+++ trunk/packages/srst2/trunk/debian/mans/VFDB_cdhit_to_csv.1 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,29 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH VFDB_CDHIT_TO_CSV "1" "June 2016" "VFDB_cdhit_to_csv 0.1.8" "User Commands"
+.SH NAME
+VFDB_cdhit_to_csv \- Parse cdhit results
+.SH SYNOPSIS
+.B VFDB_cdhit_to_csv
+[\-h] \fB\-\-cluster_file\fR CLUSTER_FILE \fB\-\-infile\fR INFILE
+\fB\-\-outfile\fR OUTFILE
+.SH DESCRIPTION
+This tool is part of the SRST2 suite.
+.P
+Output a comma-separated table of alleles, their inferred gene name (from annotation)
+and their 90% cluster from CD-HIT analysis
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-cluster_file\fR CLUSTER_FILE
+cd hit output file (.clstr)
+.TP
+\fB\-\-infile\fR INFILE
+raw sequences file that was input to cdhit (fasta)
+.TP
+\fB\-\-outfile\fR OUTFILE
+output file (csv)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/srst2/trunk/debian/mans/VFDBgenus.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/VFDBgenus.1 (rev 0)
+++ trunk/packages/srst2/trunk/debian/mans/VFDBgenus.1 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH VFDBGENUS "1" "June 2016" "VFDBgenus 0.1.8" "User Commands"
+.SH NAME
+VFDBgenus \- Extract virulence genes by genus from the VFDB database
+.SH SYNOPSIS
+.B VFDBgenus
+[\-h] \fB\-\-infile\fR INFILE [\-\-genus GENUS]
+.SH DESCRIPTION
+This tool is part of the SRST2 suite.
+.P
+Extract virulence genes by genus from the VFDB database available at
+http://www.mgc.ac.cn/VFs/Down/CP_VFs.ffn.gz
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-infile\fR INFILE
+Raw VFDB sequences file (fasta, e.g. download from
+http://www.mgc.ac.cn/VFs/Down/CP_VFs.ffn.gz)
+.TP
+\fB\-\-genus\fR GENUS
+Genus to extract (if not specified, all genera will be
+extracted to individual files)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/srst2/trunk/debian/mans/csv_to_gene_db.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/csv_to_gene_db.1 (rev 0)
+++ trunk/packages/srst2/trunk/debian/mans/csv_to_gene_db.1 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH CSV_TO_GENE_DB "1" "June 2016" "csv_to_gene_db 0.1.8" "User Commands"
+.SH NAME
+csv_to_gene_db \- generate the appropriate headers for srst2
+.SH SYNOPSIS
+.B csv_to_gene_db
+[\fI\,options\/\fR]
+.SH DESCRIPTION
+This tool is part of the SRST2 suite.
+.P
+take csv table detailing clustering etc and sequences for gene DB, write as fasta
+expected csv file format:
+.IP
+seqID,clusterid,gene,allele,(DNAseq),other....
+.P
+headers in output will be srst2 compatible, ie [clusterID]__[gene]__[allele]__[seqID] [other stuff]
+sequence can be read from a specified column or from a fasta file (specify which column contains fasta header to match in seqs file)
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-t\fR TABLE_FILE, \fB\-\-table\fR=\fI\,TABLE_FILE\/\fR
+table to read (csv)
+.TP
+\fB\-o\fR OUTPUT_FILE, \fB\-\-out\fR=\fI\,OUTPUT_FILE\/\fR
+output file (fasta)
+.TP
+\fB\-s\fR SEQ_COL, \fB\-\-seq_col\fR=\fI\,SEQ_COL\/\fR
+column number containing sequences
+.TP
+\fB\-f\fR FASTA_FILE, \fB\-\-fasta\fR=\fI\,FASTA_FILE\/\fR
+fasta file to read sequences from (must specify which
+column in the table contains the sequence names that
+match the fasta file headers)
+.TP
+\fB\-c\fR HEADERS_COL, \fB\-\-headers_col\fR=\fI\,HEADERS_COL\/\fR
+column number that contains the sequence names that
+match the fasta file headers
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/srst2/trunk/debian/mans/get_all_vfdb.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/get_all_vfdb.1 (rev 0)
+++ trunk/packages/srst2/trunk/debian/mans/get_all_vfdb.1 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,16 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH GET_ALL_VFDB "1" "June 2016" "get_all_vfdb 0.1.8" "User Commands"
+.SH NAME
+get_all_vfdb \- automate generation of all the VFDB gene databases for use with srst2
+.SH SYNOPSIS
+.B get_all_vfdb
+\fI\,<vfdbfile> <outputfolder>\/\fR
+.SH DESCRIPTION
+This tool is part of the SRST2 suite.
+.P
+This is a utility that automates generation of all the VFDB gene databases for use with srst2(1).
+.SH EXAMPLE
+.IP
+get_all_vfdb ./CP_VFs.ffn ./VFDB
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/srst2/trunk/debian/mans/get_genus_vfdb.1
===================================================================
--- trunk/packages/srst2/trunk/debian/mans/get_genus_vfdb.1 (rev 0)
+++ trunk/packages/srst2/trunk/debian/mans/get_genus_vfdb.1 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,16 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH GET_GENUS_VFDB "1" "June 2016" "get_genus_vfdb 0.1.8" "User Commands"
+.SH NAME
+get_genus_vfdb \- automate generation of a VFDB gene database for a specified genus for use with srst2
+.SH SYNOPSIS
+.B get_genus_vfdb
+\fI\,<vfdbfile> <genus> <outputfolder>\/\fR
+.SH DESCRIPTION
+This tool is part of the SRST2 suite.
+.P
+This is a utility that automates generation of a VFDB gene database for a specified genus for use with srst2(1).
+.SH EXAMPLE
+.IP
+get_genus_vfdb.sh ./CP_VFs.ffn Bacillus ./VFDB
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/srst2/trunk/debian/patches/add_usr_bin_python_to_scripts.patch
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/add_usr_bin_python_to_scripts.patch (rev 0)
+++ trunk/packages/srst2/trunk/debian/patches/add_usr_bin_python_to_scripts.patch 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,32 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 31 May 2016 15:02:45 +0200
+Description: Add missing interpreter line
+
+--- a/database_clustering/VFDB_cdhit_to_csv.py
++++ b/database_clustering/VFDB_cdhit_to_csv.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python
+ '''
+ Created on 19/06/2013
+ @author: Harriet Dashnow, Kat Holt
+--- a/database_clustering/VFDBgenus.py
++++ b/database_clustering/VFDBgenus.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python
+ '''
+ Extract virulence genes by genus from the VFDB database at http://www.mgc.ac.cn/VFs/Down/CP_VFs.ffn.gz
+ '''
+--- a/database_clustering/csv_to_gene_db.py
++++ b/database_clustering/csv_to_gene_db.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python
+ # take csv table detailing clustering etc and sequences for gene DB, write as fasta
+ # expected csv file format:
+ # seqID,clusterid,gene,allele,(DNAseq),other....
+@@ -99,4 +100,4 @@ if __name__ == "__main__":
+ f.close()
+ o.close()
+
+-
+\ No newline at end of file
++
Added: trunk/packages/srst2/trunk/debian/patches/check_command_line_arguments.patch
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/check_command_line_arguments.patch (rev 0)
+++ trunk/packages/srst2/trunk/debian/patches/check_command_line_arguments.patch 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,32 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 07 Dec 2015 14:37:55 +0100
+Description: Check command line arguments before processing
+
+--- a/database_clustering/get_all_vfdb.sh
++++ b/database_clustering/get_all_vfdb.sh
+@@ -5,6 +5,11 @@
+ #example usage:
+ #/srst2/database_clustering/get_all_vfdb.sh ./CP_VFs.ffn ./VFDB
+
++if [ $# != 2 ] ; then
++ echo "Usage: `basename $0` <vfdbfile> <outputfolder>"
++ exit 1
++fi
++
+ VFDBFILE=$(readlink -e $1)
+ OUTPUTFOLDER=$2
+ #get the srst2/database_clustering folder where all the other python scripts live side-by-side with this one
+--- a/database_clustering/get_genus_vfdb.sh
++++ b/database_clustering/get_genus_vfdb.sh
+@@ -4,6 +4,11 @@
+ #example usage:
+ #/srst2/database_clustering/get_genus_vfdb.sh ./CP_VFs.ffn Bacillus ./VFDB
+
++if [ $# != 3 ] ; then
++ echo "Usage: `basename $0` <vfdbfile> <genus> <outputfolder>"
++ exit 1
++fi
++
+ VFDBFILE=$(readlink -e $1)
+ GENUS=$2
+ OUTPUTFOLDER=$3
Added: trunk/packages/srst2/trunk/debian/patches/series
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/series (rev 0)
+++ trunk/packages/srst2/trunk/debian/patches/series 2016-06-01 22:19:24 UTC (rev 22071)
@@ -0,0 +1,2 @@
+check_command_line_arguments.patch
+add_usr_bin_python_to_scripts.patch
Modified: trunk/packages/srst2/trunk/debian/rules
===================================================================
--- trunk/packages/srst2/trunk/debian/rules 2016-06-01 21:51:40 UTC (rev 22070)
+++ trunk/packages/srst2/trunk/debian/rules 2016-06-01 22:19:24 UTC (rev 22071)
@@ -16,6 +16,8 @@
dh_install
mv debian/$(DEBPKGNAME)/usr/lib/*/dist-packages/$(DEBPKGNAME)/* debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)
rm -rf debian/*/usr/bin/*.py debian/$(DEBPKGNAME)/usr/lib/*/dist-packages/
+ # fix line endings to make sure Python interpreter will be found
+ find debian/*/usr/share -name "VFDB*" -exec dos2unix \{\} \;
override_dh_fixperms:
dh_fixperms
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