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()