This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.datatypes.converters.interval_to_tabix_converter

#!/usr/bin/env python

Uses pysam to index a bgzipped interval file with tabix
Supported presets: bed, gff, vcf

usage: %prog in_file out_file
import optparse
import os
import sys

from pysam import ctabix

[docs]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, 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, 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.")
if __name__ == "__main__": main()