# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks jeremy.goecks@emory.edu # Date 1279227794 14400 # Node ID 067e34574408d42d18cbf91b78e2ee6046a4ef01 # Parent e56cc2ed66423b51249eb0bf3f5f9f7ccd774bce Fix bug so that fasta identifier produced by 'extract genomic dna' tool for GFF files is consistent with GFF coordinates.

--- a/tools/extract/extract_genomic_dna.py +++ b/tools/extract/extract_genomic_dna.py @@ -158,6 +158,8 @@ def __main__(): if output_format == "fasta" : l = len( sequence ) c = 0 + if gff_format: + start, end = convert_bed_coords_to_gff( [ start, end ] ) fields = [dbkey, str( chrom ), str( start ), str( end ), strand] meta_data = "_".join( fields ) fout.write( ">%s\n" % meta_data )