#!/usr/bin/env python
"""
Uses pysam to index a bgzipped interval file with tabix
Supported presets: bed, gff, vcf
usage: %prog in_file out_file
"""
from galaxy import eggs
import pkg_resources; pkg_resources.require( "pysam" )
import ctabix, subprocess, tempfile, sys, os, 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, index_fname, out_fname = args
# Create index.
if options.preset:
# Preset type.
ctabix.tabix_index(filename=index_fname, preset=options.preset, keep_original=True,
already_compressed=True, index_filename=out_fname)
else:
# For interval files; column indices are 0-based.
ctabix.tabix_index(filename=index_fname, seq_col=(options.chrom_col - 1),
start_col=(options.start_col - 1), end_col=(options.end_col - 1),
keep_original=True, already_compressed=True, index_filename=out_fname)
if os.path.getsize(index_fname) == 0:
sys.stderr.write("The converted tabix index file is empty, meaning the input data is invalid.")
if __name__ == "__main__":
main()