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Changeset 1471:1958657d8f8d

Timestamp:

08/12/08 10:04:28 (3 months ago)

Author:

Greg Von Kuster <greg@bx.psu.edu>

branch:

default

Message:

Fix for interval2maf.py when metadata missing strand column value.

Files:

r1356	r1471
55	55	if options.chromCol: chromCol = int( options.chromCol ) - 1
56	56	else:
57		print >>sys.stderr, "Chromosome column ~~has not been specified~~."
	57	print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes."
58	58	sys.exit()
59	59
60	60	if options.startCol: startCol = int( options.startCol ) - 1
61	61	else:
62		print >>sys.stderr, "Start column ~~has not been specified~~."
	62	print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes."
63	63	sys.exit()
64	64
65	65	if options.endCol: endCol = int( options.endCol ) - 1
66	66	else:
67		print >>sys.stderr, "End column ~~has not been specified~~."
	67	print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes."
68	68	sys.exit()
69	69
70	70	if options.strandCol: strandCol = int( options.strandCol ) - 1
71	71	else:
72		print >>sys.stderr, "Strand column has not been specified."
73		sys.exit()
	72	strandCol = -1
74	73
75	74	if options.interval_file: interval_file = options.interval_file