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

import pysam


[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) pysam.tabix_compress(input_fname, output_fname, force=True) # Column indices are 0-based. pysam.tabix_index(output_fname, seq_col=options.chrom_col, start_col=options.start_col, end_col=options.end_col)
if __name__ == "__main__": main()