/lib/galaxy/datatypes/converters/bgzip.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 47 lines · 32 code · 7 blank · 8 comment · 7 complexity · 86bcce9063f17ffa9ba824298b917b64 MD5 · raw file
- #!/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
- 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()