https://github.com/galaxyproject/galaxy
Tip revision: 71ebf96cba8483a91c197241b161fa61a4fe7fe8 authored by John Chilton on 15 January 2015, 21:01:18 UTC
Bugfix: Skip extra wrapping around template-style macros.
Bugfix: Skip extra wrapping around template-style macros.
Tip revision: 71ebf96
maf_by_block_number.py
#!/usr/bin/env python
#Dan Blankenberg
"""
Reads a list of block numbers and a maf. Produces a new maf containing the
blocks specified by number.
"""
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from galaxy.tools.util import maf_utilities
import bx.align.maf
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
input_block_filename = sys.argv[1].strip()
input_maf_filename = sys.argv[2].strip()
output_filename1 = sys.argv[3].strip()
block_col = int( sys.argv[4].strip() ) - 1
if block_col < 0:
print >> sys.stderr, "Invalid column specified"
sys.exit(0)
species = maf_utilities.parse_species_option( sys.argv[5].strip() )
maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
#we want to maintain order of block file and write blocks as many times as they are listed
failed_lines = []
for ctr, line in enumerate( open( input_block_filename, 'r' ) ):
try:
block_wanted = int( line.split( "\t" )[block_col].strip() )
except:
failed_lines.append( str( ctr ) )
continue
try:
for count, block in enumerate( bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) ):
if count == block_wanted:
if species:
block = block.limit_to_species( species )
maf_writer.write( block )
break
except:
print >>sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
if len( failed_lines ) > 0: print "Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) )
if __name__ == "__main__": __main__()