[med-svn] [iva] 01/05: New upstream version 1.0.9+ds
Sascha Steinbiss
satta at debian.org
Mon Jan 29 13:56:09 UTC 2018
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository iva.
commit 1299970d689c88524024cb3d5010be7fb683c833
Author: Sascha Steinbiss <satta at debian.org>
Date: Fri Jan 26 11:43:36 2018 +0100
New upstream version 1.0.9+ds
---
.travis.yml | 9 +++
AUTHORS | 4 +-
LICENSE | 4 ++
install_dependencies.sh | 2 +-
iva/external_progs.py | 2 +-
iva/tests/external_progs_test.py | 142 +++++++++++++++++++++++++++++++++++++--
setup.py | 2 +-
7 files changed, 155 insertions(+), 10 deletions(-)
diff --git a/.travis.yml b/.travis.yml
index aefa37f..f0e6ea0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,6 +11,15 @@ cache:
- "$HOME/.cache/pip"
python:
- "3.4"
+ - "3.5"
+ - "3.6"
+env:
+ - SAMTOOLS_VERSION=1.3
+ - SAMTOOLS_VERSION=1.3.1
+ - SAMTOOLS_VERSION=1.4
+ - SAMTOOLS_VERSION=1.4.1
+ - SAMTOOLS_VERSION=1.5
+ - SAMTOOLS_VERSION=1.6
sudo: false
install:
- "source ./install_dependencies.sh"
diff --git a/AUTHORS b/AUTHORS
index 711ae85..e17462d 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1 +1,3 @@
-Martin Hunt (mh12 at sanger.ac.uk)
+Martin Hunt (path-help at sanger.ac.uk)
+Andrew J. Page (path-help at sanger.ac.uk)
+Sascha Steinbiss (path-help at sanger.ac.uk)
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
index 70566f2..70b4768 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,3 +1,7 @@
+Copyright (c) 2014 - 2017 by Genome Research Ltd.
+
+This is free software, licensed under:
+
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
diff --git a/install_dependencies.sh b/install_dependencies.sh
index b306373..a6bd04f 100755
--- a/install_dependencies.sh
+++ b/install_dependencies.sh
@@ -6,7 +6,7 @@ start_dir=$(pwd)
KMC_VERSION=2.3.0
MUMMER_VERSION=3.23
-SAMTOOLS_VERSION=1.3
+SAMTOOLS_VERSION=${SAMTOOLS_VERSION:-"1.3"}
SMALT_VERSION=0.7.6
KMC_DOWNLOAD_URL=http://sun.aei.polsl.pl/REFRESH/kmc/downloads/${KMC_VERSION}/linux/kmc
diff --git a/iva/external_progs.py b/iva/external_progs.py
index a63d84b..4f17fce 100644
--- a/iva/external_progs.py
+++ b/iva/external_progs.py
@@ -37,7 +37,7 @@ prog_to_version_cmd = {
'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
'smalt': ('smalt version', re.compile('^Version: (.*)$')),
- 'samtools': ('samtools', re.compile('^Version: ([^ ]+)')),
+ 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')),
}
diff --git a/iva/tests/external_progs_test.py b/iva/tests/external_progs_test.py
index 8795f33..7a1cbbe 100644
--- a/iva/tests/external_progs_test.py
+++ b/iva/tests/external_progs_test.py
@@ -19,28 +19,158 @@ class TestExternalProgs(unittest.TestCase):
def test_kmc_in_path(self):
'''Test kmc in path'''
self.assertTrue(external_progs.is_in_path('kmc'), 'Error! Did not find kmc in your path! Please install kmc')
-
+
def test_kmc_dump_in_path(self):
'''Test kmc_dump in path'''
self.assertTrue(external_progs.is_in_path('kmc_dump'), 'Error! Did not find kmc_dump in your path! Please install kmc')
-
+
def test_nucmer_in_path(self):
'''Test nucmer in path'''
self.assertTrue(external_progs.is_in_path('nucmer'), 'Error! Did not find nucmer in your path! Please install MUMmer')
-
+
def test_delta_filter_in_path(self):
'''Test delta-filter in path'''
self.assertTrue(external_progs.is_in_path('delta-filter'), 'Error! Did not find delta-filter in your path! Please install MUMmer')
-
+
def test_show_coords_in_path(self):
'''Test show-coords in path'''
self.assertTrue(external_progs.is_in_path('show-coords'), 'Error! Did not find show-coords in your path! Please install MUMmer')
-
+
def test_samtools_in_path(self):
'''Test samtools in path'''
self.assertTrue(external_progs.is_in_path('samtools'), 'Error! Did not find samtools in your path! Please install samtools')
-
+
def test_smalt_in_path(self):
'''Test smalt in path'''
self.assertTrue(external_progs.is_in_path('smalt'), 'Error! Did not find smalt in your path! Please install smalt')
+
+ def test_r_version(self):
+ '''Test R versions'''
+ self.assertEqual('3.4.0', self.check_regex_version_extraction('R', """
+R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
+Copyright (C) 2017 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
+ """ ))
+
+ self.assertEqual('3.3.2', self.check_regex_version_extraction('R', """
+R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
+Copyright (C) 2016 The R Foundation for Statistical Computing
+Platform: x86_64-apple-darwin13.4.0 (64-bit)
+ """ ))
+
+ self.assertEqual('3.2.2', self.check_regex_version_extraction('R', """
+R version 3.2.2 (2015-08-14) -- "Fire Safety"
+Copyright (C) 2015 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
+ """ ))
+
+ self.assertEqual('3.1.2', self.check_regex_version_extraction('R', """
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
+ """ ))
+
+ self.assertEqual('3.0.0', self.check_regex_version_extraction('R', """
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
+ """ ))
+
+ self.assertEqual('2.15.2', self.check_regex_version_extraction('R', """
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+ """ ))
+
+
+ def test_blastn_version(self):
+ '''Test blastn version'''
+ self.assertEqual('2.7.0+', self.check_regex_version_extraction('blastn', """
+blastn: 2.7.0+
+ Package: blast 2.7.0, build Sep 12 2017 15:51:33
+ """ ))
+ self.assertEqual('2.6.0+', self.check_regex_version_extraction('blastn', """
+blastn: 2.6.0+
+ Package: blast 2.6.0, build Aug 23 2017 22:18:50
+ """ ))
+ self.assertEqual('2.2.31+', self.check_regex_version_extraction('blastn', """
+blastn: 2.2.31+
+Package: blast 2.2.31, build Jul 6 2015 15:14:27
+ """ ))
+
+ def test_makeblastdb_version(self):
+ '''Test makeblastdb version'''
+ self.assertEqual('2.7.0+', self.check_regex_version_extraction('makeblastdb', """
+makeblastdb: 2.7.0+
+ Package: blast 2.7.0, build Sep 12 2017 15:51:33
+ """ ))
+ self.assertEqual('2.6.0+', self.check_regex_version_extraction('makeblastdb', """
+makeblastdb: 2.6.0+
+ Package: blast 2.6.0, build Aug 23 2017 22:18:50
+ """ ))
+ self.assertEqual('2.2.31+', self.check_regex_version_extraction('makeblastdb', """
+makeblastdb: 2.2.31+
+Package: blast 2.2.31, build Jul 6 2015 15:14:27
+ """ ))
+
+ def test_kmc_version(self):
+ '''Test kmc version'''
+ self.assertTrue(external_progs.get_version('kmc',must_be_in_path=True))
+ self.assertEqual('2.3.0', self.check_regex_version_extraction('kmc', """
+K-Mer Counter (KMC) ver. 2.3.0 (2015-08-21)
+ """ ))
+ self.assertEqual('3.0.0', self.check_regex_version_extraction('kmc', """
+K-Mer Counter (KMC) ver. 3.0.0 (2017-01-28)
+ """ ))
+
+ def test_kmc_dump_version(self):
+ '''Test kmc_dump version'''
+ self.assertTrue(external_progs.get_version('kmc_dump',must_be_in_path=True))
+ self.assertEqual('3.0.0', self.check_regex_version_extraction('kmc_dump', """
+KMC dump ver. 3.0.0 (2017-01-28)
+ """ ))
+ self.assertEqual('2.3.0', self.check_regex_version_extraction('kmc_dump', """
+KMC dump ver. 2.3.0 (2015-08-21)
+ """ ))
+
+ def test_nucmer_version(self):
+ '''Test nucmer version'''
+ self.assertTrue(external_progs.get_version('nucmer',must_be_in_path=True))
+ self.assertEqual('3.1', self.check_regex_version_extraction('nucmer', """
+nucmer
+NUCmer (NUCleotide MUMmer) version 3.1
+ """ ))
+
+ def test_samtools_version(self):
+ '''Test samtools version'''
+ self.assertTrue(external_progs.get_version('samtools', must_be_in_path=True))
+ self.assertEqual('1.6', self.check_regex_version_extraction('samtools', """
+samtools 1.6
+Using htslib 1.6
+Copyright (C) 2017 Genome Research Ltd.""" ))
+
+ def test_samtools_original_version(self):
+ '''Test samtools original version'''
+ self.assertEqual('0.1.19', self.check_regex_version_extraction('samtools', """
+Program: samtools (Tools for alignments in the SAM format)
+Version: 0.1.19-44428cd
+Usage: samtools <command> [options]""" ))
+
+ def test_smalt_version(self):
+ '''Test smalt version'''
+ self.assertTrue(external_progs.get_version('smalt',must_be_in_path=True))
+ self.assertEqual('0.7.6', self.check_regex_version_extraction('smalt', """
+ SMALT - Sequence Mapping and Alignment Tool
+Version: 0.7.6
+Date: 21-03-2014""" ))
+
+ def check_regex_version_extraction(self, prog, raw_version_output ):
+ cmd, regex = external_progs.prog_to_version_cmd[prog]
+ raw_output_lines = raw_version_output.splitlines()
+ for line in raw_output_lines:
+ hits = regex.search(line)
+ if hits:
+ return str(hits.group(1))
+ return None
diff --git a/setup.py b/setup.py
index 5269000..31499ae 100644
--- a/setup.py
+++ b/setup.py
@@ -47,7 +47,7 @@ if not found_all_progs:
setup(
name='iva',
- version='1.0.8',
+ version='1.0.9',
description='Iterative Virus Assembler',
packages = find_packages(),
package_data={'iva': ['gage/*', 'ratt/*', 'read_trim/*', 'test_run_data/*']},
--
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