1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/c3680f58e97d/ changeset: c3680f58e97d user: dan date: 2011-09-23 15:36:57 summary: MAF stats tool will now skip intervals with length less 1. affected #: 1 file (-1 bytes)
--- a/tools/maf/maf_stats.py Fri Sep 23 08:39:53 2011 -0400 +++ b/tools/maf/maf_stats.py Fri Sep 23 09:36:57 2011 -0400 @@ -55,12 +55,16 @@ out = open(output_filename, 'w')
num_region = None + num_bad_region = 0 species_summary = {} total_length = 0 #loop through interval file for num_region, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_interval_filename, 'r' ), chrom_col = chr_col, start_col = start_col, end_col = end_col, fix_strand = True, return_header = False, return_comments = False ) ): src = "%s.%s" % ( dbkey, region.chrom ) region_length = region.end - region.start + if region_length < 1: + num_bad_region += 1 + continue total_length += region_length coverage = { dbkey: BitSet( region_length ) }
@@ -99,6 +103,8 @@ out.close() if num_region is not None: print "%i regions were processed with a total length of %i." % ( num_region + 1, total_length ) + if num_bad_region: + print "%i regions were invalid." % ( num_bad_region ) maf_utilities.remove_temp_index_file( index_filename )
if __name__ == "__main__": __main__()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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