def runBAMtoJunctionBED(paths_to_run): bamfile_dir,bed_reference_dir,output_bedfile_path = paths_to_run output_bedfile_path = string.replace(bamfile_dir,'.bam','__junction.bed') #if os.path.exists(output_bedfile_path) == False: ### Only run if the file doesn't exist results = BAMtoJunctionBED.parseJunctionEntries(bamfile_dir,multi=True) #else: print output_bedfile_path, 'already exists.' return results
def runBAMtoJunctionBED(paths_to_run): bamfile_dir, bed_reference_dir, output_bedfile_path = paths_to_run output_bedfile_path = string.replace(bamfile_dir, '.bam', '__junction.bed') #if os.path.exists(output_bedfile_path) == False: ### Only run if the file doesn't exist results = BAMtoJunctionBED.parseJunctionEntries(bamfile_dir, multi=True) #else: print output_bedfile_path, 'already exists.' return results