Package: python-cogent / 1.9-14

accept_newer_cdhit.patch Patch series | download
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Author: Tim Booth <tbooth@ceh.ac.uk>
Last-Changed: Fri, 25 Apr 2014 17:27:42 +0100
Description: Get Cogent to work with newer CD-HIT that doesn't leave
 a temporary file sitting around.  This patch has only been quickly tested and
 there may be deeper issues.

--- PyCogent-1.5.3.orig/cogent/app/cd_hit.py
+++ PyCogent-1.5.3/cogent/app/cd_hit.py
@@ -257,7 +257,10 @@
     # perform cleanup
     res.cleanUp()
     shutil.rmtree(working_dir)
-    remove(params['-o'] + '.bak.clstr')
+    try:
+	remove(params['-o'] + '.bak.clstr')
+    except OSError:
+	pass #maybe there was no file
 
     return remapped_clusters
 
@@ -299,7 +302,10 @@
     # perform cleanup
     res.cleanUp()
     shutil.rmtree(working_dir)
-    remove(params['-o'] + '.bak.clstr')
+    try:
+	remove(params['-o'] + '.bak.clstr')
+    except OSError:
+	pass #maybe there was no file
 
     return SequenceCollection(new_seqs, MolType=moltype)