Source code for galaxy.datatypes.converters.bgzip

#!/usr/bin/env python

"""
Uses pysam to bgzip a file

usage: %prog in_file out_file
"""
import optparse
import subprocess
import tempfile

import pysam


[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, output_fname = args tmpfile = tempfile.NamedTemporaryFile() sort_params = None if options.chrom_col and options.start_col and options.end_col: sort_params = [ "sort", "-k%(i)s,%(i)s" % {'i': options.chrom_col}, "-k%(i)i,%(i)in" % {'i': options.start_col}, "-k%(i)i,%(i)in" % {'i': options.end_col} ] elif options.preset == "bed": sort_params = ["sort", "-k1,1", "-k2,2n", "-k3,3n"] elif options.preset == "vcf": sort_params = ["sort", "-k1,1", "-k2,2n"] elif options.preset == "gff": sort_params = ["sort", "-s", "-k1,1", "-k4,4n"] # stable sort on start column # Skip any lines starting with "#" and "track" grepped = subprocess.Popen(["grep", "-e", "^\"#\"", "-e", "^track", "-v", input_fname], stderr=subprocess.PIPE, stdout=subprocess.PIPE) after_sort = subprocess.Popen(sort_params, stdin=grepped.stdout, stderr=subprocess.PIPE, stdout=tmpfile) grepped.stdout.close() output, err = after_sort.communicate() pysam.tabix_compress(tmpfile.name, output_fname, force=True)
if __name__ == "__main__": main()