def main(): # Read options, args. parser = optparse.OptionParser() parser.add_option('-c', '--chr-col', type='int', dest='chrom_col', default=1) parser.add_option('-s', '--start-col', type='int', dest='start_col', default=2) parser.add_option('-e', '--end-col', type='int', dest='end_col', default=3) (options, args) = parser.parse_args() input_fname, output_fname = args # Make column indices 0-based. options.chrom_col -= 1 options.start_col -= 1 options.end_col -= 1 # Do conversion. index = Indexes() offset = 0 for line in open(input_fname, "r"): feature = line.strip().split() if not feature or feature[0].startswith("track") or feature[0].startswith("#"): offset += len(line) continue chrom = feature[options.chrom_col] chrom_start = int(feature[options.start_col]) chrom_end = int(feature[options.end_col]) index.add(chrom, chrom_start, chrom_end, offset) offset += len(line) index.write(open(output_fname, "w"))
def main(): # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() in_file, out_file = args # Do conversion. index = Indexes() reader = galaxy_utils.sequence.vcf.Reader( open( in_file ) ) offset = reader.metadata_len for vcf_line in reader: # VCF format provides a chrom and 1-based position for each variant. # IntervalIndex expects 0-based coordinates. index.add( vcf_line.chrom, vcf_line.pos - 1, vcf_line.pos, offset ) offset += len( vcf_line.raw_line ) index.write( open( out_file, "w" ) )
def main(): # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() in_file, out_file = args # Do conversion. index = Indexes() reader = galaxy_utils.sequence.vcf.Reader(open(in_file)) offset = reader.metadata_len for vcf_line in reader: # VCF format provides a chrom and 1-based position for each variant. # IntervalIndex expects 0-based coordinates. index.add(vcf_line.chrom, vcf_line.pos - 1, vcf_line.pos, offset) offset += len(vcf_line.raw_line) index.write(open(out_file, "w"))
def main(): # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() input_fname, output_fname = args # Do conversion. index = Indexes() offset = 0 for line in open( input_fname, "r" ): chrom, start = line.split()[ 0:2 ] # Pileup format is 1-based. start = int( start ) - 1 index.add( chrom, start, start + 1, offset ) offset += len( line ) index.write( open(output_fname, "w") )
def main(): # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() input_fname, output_fname = args # Do conversion. index = Indexes() offset = 0 for line in open(input_fname, "r"): chrom, start = line.split()[0:2] # Pileup format is 1-based. start = int(start) - 1 index.add(chrom, start, start + 1, offset) offset += len(line) index.write(open(output_fname, "w"))
def main(): # Arguments input_fname, out_fname = sys.argv[1:] # Do conversion. index = Indexes() offset = 0 reader_wrapper = GFFReaderWrapper( fileinput.FileInput( input_fname ), fix_strand=True ) for feature in list( reader_wrapper ): # Add feature; index expects BED coordinates. if isinstance( feature, GenomicInterval ): convert_gff_coords_to_bed( feature ) index.add( feature.chrom, feature.start, feature.end, offset ) # Always increment offset, even if feature is not an interval and hence # not included in the index. offset += feature.raw_size index.write( open(out_fname, "w") )
def main(): input_fname = sys.argv[1] out_fname = sys.argv[2] index = Indexes() offset = 0 for line in open(input_fname, "r"): feature = line.strip().split() if not feature or feature[0].startswith("track") or feature[0].startswith("#"): offset += len(line) continue chrom = feature[0] chrom_start = int(feature[1]) chrom_end = int(feature[2]) index.add( chrom, chrom_start, chrom_end, offset ) offset += len(line) index.write( open(out_fname, "w") )
def main(): # Arguments input_fname, out_fname = sys.argv[1:] # Do conversion. index = Indexes() offset = 0 reader_wrapper = GFFReaderWrapper(fileinput.FileInput(input_fname), fix_strand=True) for feature in list(reader_wrapper): # Add feature; index expects BED coordinates. if isinstance(feature, GenomicInterval): convert_gff_coords_to_bed(feature) index.add(feature.chrom, feature.start, feature.end, offset) # Always increment offset, even if feature is not an interval and hence # not included in the index. offset += feature.raw_size index.write(open(out_fname, "wb"))
def main(): input_fname = sys.argv[1] out_fname = sys.argv[2] index = Indexes() offset = 0 for line in open(input_fname, "r"): feature = line.strip().split() if not feature or feature[0].startswith( "track") or feature[0].startswith("#"): offset += len(line) continue chrom = feature[0] chrom_start = int(feature[1]) chrom_end = int(feature[2]) index.add(chrom, chrom_start, chrom_end, offset) offset += len(line) index.write(open(out_fname, "w"))