[med-svn] [ariba] 01/02: New upstream version 2.9.3+ds

[Sascha Steinbiss]

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

satta pushed a commit to branch upstream
in repository ariba.

commit db1f8f07c0943120e89024d8bd0c0117305c46bb
Author: Sascha Steinbiss <satta at debian.org>
Date:   Fri Apr 28 16:52:08 2017 +0200

    New upstream version 2.9.3+ds
---
 ariba/pubmlst_getter.py                          | 10 +++++++++-
 ariba/tests/data/pubmlst_rename_seqs.expected.fa | 10 ++++++++++
 ariba/tests/data/pubmlst_rename_seqs.in.fa       | 10 ++++++++++
 setup.py                                         |  2 +-
 4 files changed, 30 insertions(+), 2 deletions(-)

diff --git a/ariba/pubmlst_getter.py b/ariba/pubmlst_getter.py
index 0f794d1..6ac8bf5 100644
--- a/ariba/pubmlst_getter.py
+++ b/ariba/pubmlst_getter.py
@@ -1,4 +1,5 @@
 import tempfile
+import re
 import time
 import os
 import shutil
@@ -79,9 +80,16 @@ class PubmlstGetter:
     def _rename_seqs_in_fasta(cls, infile, outfile):
         f = pyfastaq.utils.open_file_write(outfile)
         file_reader = pyfastaq.sequences.file_reader(infile)
+        nodot_regex = re.compile(r'^.*(?P<separator>[^.0-9])[0-9]+$')
 
         for seq in file_reader:
-            seq.id = seq.id.replace('_', '.').replace('-', '.')
+            if seq.id.startswith('Oxf.'):
+                seq.id = 'Oxf_' + seq.id[4:]
+
+            regex_match = nodot_regex.match(seq.id)
+            if regex_match is not None:
+                seq.id = '.'.join(seq.id.rsplit(regex_match.groupdict()['separator'], maxsplit=1))
+
             print(seq, file=f)
 
         pyfastaq.utils.close(f)
diff --git a/ariba/tests/data/pubmlst_rename_seqs.expected.fa b/ariba/tests/data/pubmlst_rename_seqs.expected.fa
index 7e7fa08..d6cb400 100644
--- a/ariba/tests/data/pubmlst_rename_seqs.expected.fa
+++ b/ariba/tests/data/pubmlst_rename_seqs.expected.fa
@@ -4,3 +4,13 @@ ACGT
 AAAA
 >gene.3
 CCCC
+>foo_gene.4
+TTTT
+>Oxf_gltA.42
+A
+>Oxf_gltA.43
+C
+>Oxf_gltA.44
+G
+>Oxf_gltA.45
+T
diff --git a/ariba/tests/data/pubmlst_rename_seqs.in.fa b/ariba/tests/data/pubmlst_rename_seqs.in.fa
index 8b1a4c7..16c443e 100644
--- a/ariba/tests/data/pubmlst_rename_seqs.in.fa
+++ b/ariba/tests/data/pubmlst_rename_seqs.in.fa
@@ -4,3 +4,13 @@ ACGT
 AAAA
 >gene.3
 CCCC
+>foo_gene.4
+TTTT
+>Oxf.gltA.42
+A
+>Oxf.gltA-43
+C
+>Oxf.gltA_44
+G
+>Oxf.gltA?45
+T
diff --git a/setup.py b/setup.py
index 7c673d0..1f1d390 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='2.9.2',
+    version='2.9.3',
     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