[med-svn] r23343 - in trunk/packages/pynast/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-12-21 07:23:44 +0000 (Wed, 21 Dec 2016)
New Revision: 23343

Added:
   trunk/packages/pynast/trunk/debian/patches/accommodate_blast+.patch
Modified:
   trunk/packages/pynast/trunk/debian/changelog
   trunk/packages/pynast/trunk/debian/patches/series
Log:
Fix test failures with new version of ncbi-blast+


Modified: trunk/packages/pynast/trunk/debian/changelog
===================================================================
--- trunk/packages/pynast/trunk/debian/changelog	2016-12-20 21:15:32 UTC (rev 23342)
+++ trunk/packages/pynast/trunk/debian/changelog	2016-12-21 07:23:44 UTC (rev 23343)
@@ -1,3 +1,11 @@
+pynast (1.2.2-2) UNRELEASED; urgency=medium
+
+  * Fix test failures with new version of ncbi-blast+ (Thanks for the patch to
+    Aaron M. Ucko)
+    Closes: #848735
+
+ -- Andreas Tille <tille at debian.org>  Wed, 21 Dec 2016 08:21:44 +0100
+
 pynast (1.2.2-1) unstable; urgency=medium
 
   * New upsteam version now on Github (adapted d/watch)

Added: trunk/packages/pynast/trunk/debian/patches/accommodate_blast+.patch
===================================================================
--- trunk/packages/pynast/trunk/debian/patches/accommodate_blast+.patch	                        (rev 0)
+++ trunk/packages/pynast/trunk/debian/patches/accommodate_blast+.patch	2016-12-21 07:23:44 UTC (rev 23343)
@@ -0,0 +1,43 @@
+Description: Adapt to the modern BLAST engine and BLAST+ legacy_blast wrapper.
+* Specify an explicit gap extension cost (2) to accompany the explicit
+  mismatch penalty.
+* Reduce the word size to the traditional value of 11 so the test
+  cases can succeed.
+* Stop trying to request the old engine.
+* Accommodate minor output format changes between legacy BLAST and
+  BLAST+.
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: Tue, 20 Dec 2016 18:07:46 -0500
+Bug-Debian: https://bugs.debian.org/848735
+
+--- a/pynast/util.py
++++ b/pynast/util.py
+@@ -147,7 +147,7 @@ def blast_align_unaligned_seqs(seqs,
+     
+     # Note: -S 1 indicated that we don't want to blast both orientations -- at
+     # this would be different behavior than other pairwise aligners.
+-    bl2seq_res = system('bl2seq -i %s -j %s -o %s -F F -S 1 -q -1 -p blastn -VT' %\
++    bl2seq_res = system('bl2seq -i %s -j %s -o %s -F F -S 1 -q -1 -E 2 -W 11 -p blastn' %\
+      (in_filepath1,in_filepath2,out_filepath))
+     if bl2seq_res != 0:
+         raise RuntimeError, "bl2seq failed:\n %s" % bl2seq_res 
+@@ -157,16 +157,16 @@ def blast_align_unaligned_seqs(seqs,
+     blast_res = open(out_filepath)
+     in_result = False
+     for line in blast_res:
+-        if line.strip().startswith('Score'):
++        if line.strip().startswith('Score = '):
+             if in_result:
+                 break
+             else:
+                 in_result = True
+             
+-        if line.startswith('Query: '):
++        if in_result and line.startswith('Query'):
+             fields = line.split()
+             query_seq.append(fields[2].upper())
+-        elif line.startswith('Sbjct: '):
++        elif in_result and line.startswith('Sbjct'):
+             fields = line.split()
+             subject_seq.append(fields[2].upper())
+         else:

Modified: trunk/packages/pynast/trunk/debian/patches/series
===================================================================
--- trunk/packages/pynast/trunk/debian/patches/series	2016-12-20 21:15:32 UTC (rev 23342)
+++ trunk/packages/pynast/trunk/debian/patches/series	2016-12-21 07:23:44 UTC (rev 23343)
@@ -1,3 +1,4 @@
 do_not_install_privacy_breaching_scripts.patch
 skip_tests_needing_uclust.patch
 avoid_python-mpi4py_missing_warning.patch
+accommodate_blast+.patch