#!/usr/bin/env python
"""
Uses pysam to bgzip a file
usage: %prog in_file out_file
"""
from galaxy import eggs
import pkg_resources; pkg_resources.require( "pysam" )
import ctabix, subprocess, tempfile, sys, optparse
[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()
ctabix.tabix_compress(tmpfile.name, output_fname, force=True)
if __name__ == "__main__":
main()