def main():
# Read options, args.
parser = optparse.OptionParser()
parser.add_option('-c', '--chr-col', type='int', dest='chrom_col')
parser.add_option('-s', '--start-col', type='int', dest='start_col')
parser.add_option('-e', '--end-col', type='int', dest='end_col')
parser.add_option('-P', '--preset', dest='preset')
(options, args) = parser.parse_args()
input_fname, index_fname, out_fname = args
# Create index.
if options.preset:
# Preset type.
ctabix.tabix_index(filename=index_fname,
preset=options.preset,
keep_original=True,
already_compressed=True,
index_filename=out_fname)
else:
# For interval files; column indices are 0-based.
ctabix.tabix_index(filename=index_fname,
seq_col=(options.chrom_col - 1),
start_col=(options.start_col - 1),
end_col=(options.end_col - 1),
keep_original=True,
already_compressed=True,
index_filename=out_fname)
if os.path.getsize(index_fname) == 0:
sys.stderr.write(
"The converted tabix index file is empty, meaning the input data is invalid."
)
def main():
# Read options, args.
usage = "Usage: %prog [options] tabular_input_file bgzip_output_file"
parser = optparse.OptionParser(usage = usage)
parser.add_option( '-c', '--chr-col', type='int', default=0, dest='chrom_col' )
parser.add_option( '-s', '--start-col', type='int', default=1, dest='start_col' )
parser.add_option( '-e', '--end-col', type='int', default=1, dest='end_col' )
(options, args) = parser.parse_args()
if len(args) != 2:
parser.print_usage()
exit(1)
input_fname, output_fname = args
output_dir = os.path.dirname(output_fname)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
ctabix.tabix_compress(input_fname, output_fname, force=True)
# Column indices are 0-based.
ctabix.tabix_index(output_fname, seq_col=options.chrom_col,start_col=options.start_col,end_col=options.end_col)
def main():
# Read options, args.
parser = optparse.OptionParser()
parser.add_option( '-c', '--chr-col', type='int', dest='chrom_col' )
parser.add_option( '-s', '--start-col', type='int', dest='start_col' )
parser.add_option( '-e', '--end-col', type='int', dest='end_col' )
parser.add_option( '-P', '--preset', dest='preset' )
(options, args) = parser.parse_args()
input_fname, index_fname, out_fname = args
# Create index.
if options.preset:
# Preset type.
ctabix.tabix_index(filename=index_fname, preset=options.preset, keep_original=True,
already_compressed=True, index_filename=out_fname)
else:
# For interval files; column indices are 0-based.
ctabix.tabix_index(filename=index_fname, seq_col=(options.chrom_col - 1),
start_col=(options.start_col - 1), end_col=(options.end_col - 1),
keep_original=True, already_compressed=True, index_filename=out_fname)
if os.path.getsize(index_fname) == 0:
sys.stderr.write("The converted tabix index file is empty, meaning the input data is invalid.")