mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
46 lines
1.2 KiB
Python
46 lines
1.2 KiB
Python
#!/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__()
|