[med-svn] [Git][med-team/virulencefinder][master] 9 commits: New upstream version 2.0.4
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Mon Jul 5 20:51:47 BST 2021
Nilesh Patra pushed to branch master at Debian Med / virulencefinder
Commits:
6840870f by Nilesh Patra at 2021-07-06T00:40:24+05:30
New upstream version 2.0.4
- - - - -
e7ce6ace by Nilesh Patra at 2021-07-06T00:40:25+05:30
Update upstream source from tag 'upstream/2.0.4'
Update to upstream version '2.0.4'
with Debian dir ff87d0246e5bbc989e392cb0831c623ee9a1a847
- - - - -
4818e37e by Nilesh Patra at 2021-07-06T00:43:23+05:30
Update d/u/metadata, Make yamllint happy
- - - - -
1cc40f8b by Nilesh Patra at 2021-07-06T00:45:39+05:30
Bump debhelper-compat version to 13
- - - - -
0e9539b9 by Nilesh Patra at 2021-07-06T00:45:57+05:30
Declare compliance with policy 4.5.1
- - - - -
735aeb69 by Nilesh Patra at 2021-07-05T19:31:30+00:00
d/rules: dh_installman with language=C
- - - - -
257e5e70 by Nilesh Patra at 2021-07-05T19:38:35+00:00
Add manpages
- - - - -
eb566201 by Nilesh Patra at 2021-07-06T01:19:31+05:30
d/rules: Cleanup post testing (makes build reproducible)
- - - - -
132d78da by Nilesh Patra at 2021-07-06T01:19:31+05:30
Interim changelog entry
- - - - -
8 changed files:
- debian/changelog
- debian/control
- + debian/createmanpages
- + debian/manpages
- debian/rules
- debian/upstream/metadata
- + debian/virulencefinder.py.1
- virulencefinder.py
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+virulencefinder (2.0.4-1) UNRELEASED; urgency=medium
+
+ * Team Upload.
+ * New upstream version 2.0.4
+ * Update d/u/metadata, Make yamllint happy
+ * Bump debhelper-compat version to 13
+ * Declare compliance with policy 4.5.1
+ * d/rules: dh_installman with language=C
+ * Add manpages
+ * d/rules: Cleanup post testing (makes build reproducible)
+
+ -- Nilesh Patra <nilesh at debian.org> Mon, 05 Jul 2021 19:43:45 +0000
+
virulencefinder (2.0.3+git20190809.dde157a-3) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -3,13 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3,
python3-tabulate,
python3-cgecore,
ncbi-blast+ <!nocheck>
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/virulencefinder
Vcs-Git: https://salsa.debian.org/med-team/virulencefinder.git
Homepage: https://bitbucket.org/genomicepidemiology/virulencefinder
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=virulencefinder.py
+help2man --no-info --no-discard-stderr \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/rules
=====================================
@@ -3,7 +3,7 @@
# DH_VERBOSE := 1
export PYBUILD_SYSTEM=custom
-export PYBUILD_CLEAN_ARGS=rm -rf test/results_tab.tsv
+export PYBUILD_CLEAN_ARGS=rm -rf test/Hit_in_genome_seq.fsa test/Virulence_genes.fsa test/data.json test/tmp test/results_tab.tsv test/results.txt
%:
dh $@ --with python3 --buildsystem=pybuild
@@ -19,3 +19,6 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
echo "TEST FAILED"; \
fi
endif
+
+override_dh_installman:
+ dh_installman --language=C
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+---
Reference:
- Author: >
Katrine Grimstrup Joensen and Flemming Scheutz and Ole Lund and Henrik
@@ -22,3 +23,6 @@ Registry:
- Name: bio.tools
Entry: NA
Repository: https://bitbucket.org/genomicepidemiology/virulencefinder
+Bug-Database: https://bitbucket.org/genomicepidemiology/virulencefinder/issues
+Bug-Submit: https://bitbucket.org/genomicepidemiology/virulencefinder/issues/new
+Repository-Browse: https://bitbucket.org/genomicepidemiology/virulencefinder
=====================================
debian/virulencefinder.py.1
=====================================
@@ -0,0 +1,55 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH VIRULENCEFINDER.PY "1" "July 2021" "virulencefinder.py 2.0.4" "User Commands"
+.SH NAME
+virulencefinder.py \- identify virulence genes in total or partial sequenced isolates of bacteria
+.SH DESCRIPTION
+usage: virulencefinder.py [\-h] \fB\-i\fR INFILE [INFILE ...] [\-o OUTDIR]
+.TP
+[\-tmp TMP_DIR] [\-mp METHOD_PATH] [\-p DB_PATH]
+[\-d DATABASES] [\-l MIN_COV] [\-t THRESHOLD] [\-x]
+[\-\-speciesinfo_json SPECIESINFO_JSON] [\-q]
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR INFILE [INFILE ...], \fB\-\-infile\fR INFILE [INFILE ...]
+FASTA or FASTQ input files.
+.TP
+\fB\-o\fR OUTDIR, \fB\-\-outputPath\fR OUTDIR
+Path to blast output
+.TP
+\fB\-tmp\fR TMP_DIR, \fB\-\-tmp_dir\fR TMP_DIR
+Temporary directory for storage of the results from
+the external software.
+.TP
+\fB\-mp\fR METHOD_PATH, \fB\-\-methodPath\fR METHOD_PATH
+Path to method to use (kma or blastn)
+.TP
+\fB\-p\fR DB_PATH, \fB\-\-databasePath\fR DB_PATH
+Path to the databases
+.TP
+\fB\-d\fR DATABASES, \fB\-\-databases\fR DATABASES
+Databases chosen to search in \- if non is specified
+all is used
+.TP
+\fB\-l\fR MIN_COV, \fB\-\-mincov\fR MIN_COV
+Minimum coverage
+.TP
+\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
+Minimum hreshold for identity
+.TP
+\fB\-x\fR, \fB\-\-extented_output\fR
+Give extented output with allignment files, template
+and query hits in fasta and a tab seperated file with
+gene profile results
+.TP
+\fB\-\-speciesinfo_json\fR SPECIESINFO_JSON
+Argument used by the cge pipeline. It takes a list in
+json format consisting of taxonomy, from domain \->
+species. A database is chosen based on the taxonomy.
+.HP
+\fB\-q\fR, \fB\-\-quiet\fR
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
virulencefinder.py
=====================================
@@ -412,6 +412,9 @@ for db in results:
contig_res[contig_id].append([hit["query_start"], hit["query_end"],
bit_score, hit])
+ if not contig_res:
+ json_results[db_name][db] = "No hit found"
+
# Check for overlapping hits, only report the best
for contig_id, hit_lsts in contig_res.items():
@@ -456,8 +459,8 @@ for db in results:
function = ""
# Write JSON results dict
- json_results[db_name][db].update({header: {}})
- json_results[db_name][db][header] = {
+ json_results[db_name][db].update({contig_id: {}})
+ json_results[db_name][db][contig_id] = {
"virulence_gene": gene,
"identity": round(identity, 2),
"HSP_length": HSP,
@@ -483,7 +486,7 @@ userinput = {"filename(s)": args.infile,
"method": method,
"file_format": file_format}
run_info = {"date": date, "time": time}
-
+json_results=dict(sorted(json_results.items(), key=lambda x: x[0].lower()))
data[service]["user_input"] = userinput
data[service]["run_info"] = run_info
data[service]["results"] = json_results
View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16
--
View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/-/compare/fe0a8556ad20969245ac240e189fc2267cd29d32...132d78daa72aad8c51a6d03234cd6532c4f30c16
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