[med-svn] [ariba] 01/03: New upstream version 2.10.3+ds

[Sascha Steinbiss]

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

satta pushed a commit to branch master
in repository ariba.

commit e3b0c670b51015d8351ca72e627a0245d3044d7b
Author: Sascha Steinbiss <satta at debian.org>
Date:   Tue Nov 28 16:59:31 2017 +0100

    New upstream version 2.10.3+ds
---
 ariba/mlst_reporter.py                                  | 2 +-
 ariba/ref_genes_getter.py                               | 4 ++--
 ariba/report_filter.py                                  | 2 +-
 ariba/tests/data/mlst_reporter.het_snps.out.details.tsv | 2 +-
 setup.py                                                | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/ariba/mlst_reporter.py b/ariba/mlst_reporter.py
index ac86aa3..7269988 100644
--- a/ariba/mlst_reporter.py
+++ b/ariba/mlst_reporter.py
@@ -47,7 +47,7 @@ class MlstReporter:
                     depths = [int(x) for x in d['smtls_nts_depth'].split(',')]
                     depths.sort()
                     het_pc = round(100.0 * depths[-1] / sum(depths), 2)
-                    if results['hetmin'] == '.' or results['hetmin'] < het_pc:
+                    if results['hetmin'] == '.' or results['hetmin'] > het_pc:
                         results['hetmin'] = het_pc
         if len(het_data):
             results['hets'] = '.'.join(het_data)
diff --git a/ariba/ref_genes_getter.py b/ariba/ref_genes_getter.py
index fc9b859..f596e8b 100644
--- a/ariba/ref_genes_getter.py
+++ b/ariba/ref_genes_getter.py
@@ -41,7 +41,7 @@ class RefGenesGetter:
     def _get_card_versions(self, tmp_file):
         print('Getting available CARD versions')
         common.download_file('https://card.mcmaster.ca/download', tmp_file, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
-        p = re.compile(r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.gz)"''')
+        p = re.compile(r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.bz2)"''')
         versions = {}
 
         with open(tmp_file) as f:
@@ -85,7 +85,7 @@ class RefGenesGetter:
 
         print('Getting version', self.version)
         card_tarball_url = versions[key]
-        card_tarball = 'card.tar.gz'
+        card_tarball = 'card.tar.bz2'
         print('Working in temporary directory', tmpdir)
         print('Downloading data from card:', card_tarball_url, flush=True)
         common.syscall('wget -O ' + card_tarball + ' ' + card_tarball_url, verbose=True)
diff --git a/ariba/report_filter.py b/ariba/report_filter.py
index d7cf54d..957a764 100644
--- a/ariba/report_filter.py
+++ b/ariba/report_filter.py
@@ -61,7 +61,7 @@ class ReportFilter:
 
     @staticmethod
     def _load_report(infile):
-        '''Loads report file into a dictionary. Key=refrence name.
+        '''Loads report file into a dictionary. Key=reference name.
         Value = list of report lines for that reference'''
         report_dict = {}
         f = pyfastaq.utils.open_file_read(infile)
diff --git a/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv b/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv
index d654545..640cb99 100644
--- a/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv
+++ b/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv
@@ -1,3 +1,3 @@
 gene	allele	cov	pc	ctgs	depth	hetmin	hets
-gene1	1*	100.0	100.0	1	42.2	75.0	30,10.25,10,5
+gene1	1*	100.0	100.0	1	42.2	62.5	30,10.25,10,5
 gene2	2	100.0	100.0	1	40.2	.	.
diff --git a/setup.py b/setup.py
index b85411e..093be07 100644
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.10.1',
+    version='2.10.3',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*']},

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git