[hg] galaxy 1471: Fix for interval2maf.py when metadata missing ...

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[hg] galaxy 1471: Fix for interval2maf.py when metadata missing ...

greg
details:   http://www.bx.psu.edu/hg/galaxy/rev/1958657d8f8d
changeset: 1471:1958657d8f8d
user:      Greg Von Kuster <[hidden email]>
date:      Tue Aug 12 10:04:28 2008 -0400
description:
Fix for interval2maf.py when metadata missing strand column value.

1 file(s) affected in this change:

tools/maf/interval2maf.py

diffs (31 lines):

diff -r 78e84936b7a3 -r 1958657d8f8d tools/maf/interval2maf.py
--- a/tools/maf/interval2maf.py Tue Aug 12 09:18:47 2008 -0400
+++ b/tools/maf/interval2maf.py Tue Aug 12 10:04:28 2008 -0400
@@ -54,23 +54,22 @@
     
     if options.chromCol: chromCol = int( options.chromCol ) - 1
     else:
-        print >>sys.stderr, "Chromosome column has not been specified."
+        print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes."
         sys.exit()
     
     if options.startCol: startCol = int( options.startCol ) - 1
     else:
-        print >>sys.stderr, "Start column has not been specified."
+        print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes."
         sys.exit()
     
     if options.endCol: endCol = int( options.endCol ) - 1
     else:
-        print >>sys.stderr, "End column has not been specified."
+        print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes."
         sys.exit()
     
     if options.strandCol: strandCol = int( options.strandCol ) - 1
     else:
-        print >>sys.stderr, "Strand column has not been specified."
-        sys.exit()
+        strandCol = -1
     
     if options.interval_file: interval_file = options.interval_file
     else: