details:
http://www.bx.psu.edu/hg/galaxy/rev/4c3282337a4c
changeset: 2464:4c3282337a4c
user: guru
date: Tue Jul 07 12:06:35 2009 -0400
description:
A bug fix for extract genomic dna to handle invalid chromosomes correctly.
1 file(s) affected in this change:
tools/extract/extract_genomic_dna.py
diffs (21 lines):
diff -r 3a4561684257 -r 4c3282337a4c tools/extract/extract_genomic_dna.py
--- a/tools/extract/extract_genomic_dna.py Mon Jul 06 20:41:24 2009 -0400
+++ b/tools/extract/extract_genomic_dna.py Tue Jul 07 12:06:35 2009 -0400
@@ -117,7 +117,7 @@
first_invalid_line = i + 1
invalid_line = line
continue
- elif seq_path and os.path.exists( seq_path ):
+ elif seq_path and os.path.isfile( seq_path ):
if chrom in twobits:
t = twobits[chrom]
else:
@@ -133,7 +133,7 @@
invalid_line = line
continue
else:
- warning = "Chrom '%s' was not found for build '%s'.
" % ( chrom, dbkey )
+ warning = "Chromosome by name '%s' was not found for build
'%s'. " % ( chrom, dbkey )
warnings.append( warning )
skipped_lines += 1
if not invalid_line: