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: