/tools/maf/maf_reverse_complement.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 42 lines · 28 code · 5 blank · 9 comment · 5 complexity · d7574b4bca01bd02d16ab28be2f3a9cf MD5 · raw file
- #!/usr/bin/env python
-
- """
- Reads a MAF file. Produces a MAF file containing
- the reverse complement for each block in the source file.
-
- usage: %prog input_maf_file output_maf_file
- """
- #Dan Blankenberg
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "bx-python" )
- import bx.align.maf
- from galaxy.tools.util import maf_utilities
- import sys
-
- assert sys.version_info[:2] >= ( 2, 4 )
-
- def __main__():
- #Parse Command Line
- input_file = sys.argv.pop( 1 )
- output_file = sys.argv.pop( 1 )
- species = maf_utilities.parse_species_option( sys.argv.pop( 1 ) )
-
- try:
- maf_writer = bx.align.maf.Writer( open( output_file, 'w' ) )
- except:
- print sys.stderr, "Unable to open output file"
- sys.exit()
- try:
- count = 0
- for count, maf in enumerate( bx.align.maf.Reader( open( input_file ) ) ):
- maf = maf.reverse_complement()
- if species:
- maf = maf.limit_to_species( species )
- maf_writer.write( maf )
- except:
- print >>sys.stderr, "Your MAF file appears to be malformed."
- sys.exit()
- print "%i regions were reverse complemented." % count
- maf_writer.close()
-
- if __name__ == "__main__": __main__()