Simplifying handling fasta

core/pymod/core/pm3argparse.py

@@ -213,6 +213,24 @@ class PM3OptionsNamespace(object):
         if 'ALIGNMENT' in activated:
             self._PostProcessAlignment()
 
+    def _FetchAlnFromFastaOpt(self, argstr):
+        """
+        Dissasemble an argument to '--fasta' into an alignment and return.
+        """
+        # get which element of the argument list is the target identifier and
+        # which one is the filename
+        if argstr[0].startswith('trg:'):
+            trgname = argstr[0][4:]
+            seqfile = argstr[1]
+        elif argstr[1].startswith('trg:'):
+            trgname = argstr[1][4:]
+            seqfile = argstr[0]
+        else:
+            helper.MsgErrorAndExit("'--fasta %s' requires " % ' '.join(argstr)+
+                                   "one argument prefixed with 'trg:' marking "+
+                                   "the target sequence name", 11)
+        return trgname, seqfile
+
     def _PostProcessAlignment(self):
         #pylint: disable=no-member
         #pylint: disable=attribute-defined-outside-init
@@ -223,16 +241,7 @@ class PM3OptionsNamespace(object):
         self.alignments = seq.AlignmentList()
         if self.fasta:
             for src in self.fasta:
-                if src[0].startswith('trg:'):
-                    trgname = src[0][4:]
-                    seqfile = src[1]
-                elif src[1].startswith('trg:'):
-                    trgname = src[1][4:]
-                    seqfile = src[0]
-                else:
-                    helper.MsgErrorAndExit("'--fasta' requires one argument "+
-                                           "prefixed with 'trg:' marking the "+
-                                           "target sequence name", 11)
+                trgname, seqfile = self._FetchAlnFromFastaOpt(src)
                 if not len(trgname):
                     helper.MsgErrorAndExit("'--fasta' requires argument "+
                                            "'trg:' defining the "+

core/tests/test_pm3argparse.py

@@ -87,7 +87,7 @@ class PM3ArgParseTests(unittest.TestCase):
             parser.Parse(['--fasta', 'foo', 'bar'])
         self.assertEqual(ecd.exception.code, 11)
         self.assertEqual(self.log.messages['ERROR'][0],
-                         "'--fasta' requires one "+
+                         "'--fasta foo bar' requires one "+
                          "argument prefixed with 'trg:' marking the target "+
                          "sequence name")