changed from -a to --daa because the way command is printed does not …

…handle short args. TODO

bio_pieces/parallel_blast.py

@@ -128,7 +128,7 @@ def parallel_diamond(inputfile, outfile, ninst, db, task, diamondoptions):
     # format of the file
     diamond_cmd = [
         dmnd_path, task, '--threads', str(ninst), '--db', db, '--query', '{}',
-        '-a', '{}.{#}', ';', dmnd_path, 'view', '{}.{#}.daa'
+        '--daa', '{}.{#}', ';', dmnd_path, 'view', '--daa', '{}.{#}.daa'
     ]
     if len(sshlogins) > 2:
         args = ['-u', '--pipe', '--block', '10', '--recstart', '>', '--cat']
@@ -143,10 +143,10 @@ def parallel_diamond(inputfile, outfile, ninst, db, task, diamondoptions):
         if diamondoptions:
             args += shlex.split(diamondoptions)
         p = run(
-            dcmd, *args, threads=ninst, db=db, query=inputfile, a=outfile
+            dcmd, *args, threads=ninst, db=db, query=inputfile, daa=outfile
         )
         p = run(
-            dcmd, 'view', a=outfile+'.daa', _out=open(outfile,'w')
+            dcmd, 'view', daa=outfile+'.daa', _out=open(outfile,'w')
         )
 
 def run(cmd, *args, **kwargs):

tests/test_parallel_blast.py

@@ -255,13 +255,13 @@ def test_local_runs_diamond_cmd_directly(self):
         self.assertEqual(5, r1k['threads'])
         self.assertEqual(self.infile, r1k['query'])
         self.assertEqual('/path/to/dmd', r1k['db'])
-        self.assertEqual(self.outfile, r1k['a'])
+        self.assertEqual(self.outfile, r1k['daa'])
         self.assertEqual('foox', r1a[0])
         self.assertEqual(('-bar','foo'), r1a[1:])
 
         r2a,r2k = r2
         self.assertEqual('view', r2a[0])
-        self.assertEqual(self.outfile+'.daa', r2k['a'])
+        self.assertEqual(self.outfile+'.daa', r2k['daa'])
         self.assertEqual(self.mock_open.return_value, r2k['_out'])
         self.mock_open.assert_called_once_with(self.outfile,'w')