cater for specific needs of blast 2.2.16

modules/bindings/pymod/blast.py

@@ -125,6 +125,20 @@ def ParseBlastOutput(string):
     hits.append(BlastHit(hit_id, aligned_patches))
   return hits
 
+def BlastVersion(blast_location=None):
+  """
+  Returns the version of the BLAST executable, e.g. 2.2.24 as a string
+  """
+  blastall_exe=settings.Locate('blastall', explicit_file_name=blast_location)
+  blast_pipe=subprocess.Popen(blastall_exe, stdout=subprocess.PIPE,
+                              stderr=subprocess.PIPE)
+  lines=blast_pipe.stdout.readlines()
+  pattern=re.compile(r'blastall (\d+\.\d+\.\d+)\s+arguments:\s*')
+  for line in lines:
+    m=pattern.match(line)
+    if m:
+      return m.group(1)
+  raise IOError("could not determine blast version for '%s'" % blastall_exe)
 
 def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
          blast_location=None):

modules/bindings/tests/test_blast.py

@@ -26,11 +26,20 @@ class TestBlastBindings(unittest.TestCase):
   
   def testParseBlastOutput(self):
     hits=blast.Blast(self.query, 'testfiles/seqdb')
-    expected_output=[{'evalue':2.366130E-59,'bitscore':211.460,'score':537}, 
-                     {'evalue':4.808930E-59,'bitscore':210.305,'score':534}, 
-                     {'evalue':5.361450E-58,'bitscore':206.838,'score':525}, 
-                     {'evalue':3.277500E+00,'bitscore':15.0086,'score':27}, 
-                     {'evalue':9.696520E+00,'bitscore':13.4678,'score':23}]
+    blast_version=blast.BlastVersion()
+    if blast_version=='2.2.16':
+      expected_output=[{'evalue':4.808930E-59,'bitscore':210.305,'score':534}, 
+                       {'evalue':2.366130E-59,'bitscore':210.305,'score':534}, 
+                       {'evalue':5.361450E-58,'bitscore':206.068,'score':523}, 
+                       {'evalue':2.965230E+00,'bitscore':15.0086,'score':27}, 
+                       {'evalue':9.696520E+00,'bitscore':13.4678,'score':23}]
+ 
+    else:
+      expected_output=[{'evalue':2.366130E-59,'bitscore':211.460,'score':537}, 
+                       {'evalue':4.808930E-59,'bitscore':210.305,'score':534}, 
+                       {'evalue':5.361450E-58,'bitscore':206.838,'score':525}, 
+                       {'evalue':3.277500E+00,'bitscore':15.0086,'score':27}, 
+                       {'evalue':9.696520E+00,'bitscore':13.4678,'score':23}]
     self.assertEqual(len(hits), 4)
     for expected, hit in zip(expected_output, hits):
       patch=hit.aligned_patches[0]