Moved out decision for target seq name and seq file

core/pymod/core/pm3argparse.py

@@ -13,12 +13,13 @@ from ost import io, seq
 
 from promod3.core import helper
 
-def _FetchAlnFromFastaOpt(argstr):
-    """
-    Dissasemble an argument to '--fasta' into an alignment and return.
+def _GetTrgNameSeqFile(argstr):
+    """Sort out what is target name and what is the sequence file name.
+
+    With only two items in the argument string to '--fasta' we allow arbitrary
+    orders. So we have to check for the 'trg:' prefix. With this, sequence files
+    names may not start with 'trg:'.
     """
-    # 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]
@@ -35,8 +36,15 @@ def _FetchAlnFromFastaOpt(argstr):
                                "argument 'trg:' defining the "+
                                "target sequence name, empty one "+
                                "found: '%s'" % ' '.join(argstr), 14)
-    # checking that alignment file exists
     helper.FileExists("Alignment", 12, seqfile)
+
+    return trgname, seqfile
+
+def _FetchAlnFromFastaOpt(argstr):
+    """
+    Dissasemble an argument to '--fasta' into an alignment and return.
+    """
+    trgname, seqfile = _GetTrgNameSeqFile(argstr)
     # checking if alignment file has 'gz' extension
     is_gz = helper.FileGzip("Alignment", 13, seqfile)
     # loading the alignment, switch for gzip