Warning

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.tabular_to_dbnsfp

#!/usr/bin/env python
"""
Uses pysam to bgzip a file

usage: %prog in_file out_file
"""

import optparse
import os.path

from pysam import ctabix


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