Warning

This document is for an in-development version 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.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},{i}".format(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()