root/galaxy-central/tools/maf/maf_limit_to_species.py

#!/usr/bin/env python

"""
Read a maf file and write out a new maf with only blocks having the 
required species, after dropping any other species and removing
columns containing only gaps.

usage: %prog species,species2,... input_maf output_maf allow_partial min_species_per_block
"""
#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():

    species = maf_utilities.parse_species_option( sys.argv[1] )
    if species:
        spec_len = len( species )
    else:
        spec_len = 0
    try:
        maf_reader = bx.align.maf.Reader( open( sys.argv[2],'r' ) )
        maf_writer = bx.align.maf.Writer( open( sys.argv[3],'w' ) )
    except:
        print >>sys.stderr, "Your MAF file appears to be malformed."
        sys.exit()
    allow_partial = False
    if int( sys.argv[4] ): allow_partial = True
    min_species_per_block = int( sys.argv[5] )
    
    maf_blocks_kept = 0
    for m in maf_reader:
        if species:
            m = m.limit_to_species( species )
        m.remove_all_gap_columns()
        spec_in_block_len = len( maf_utilities.get_species_in_block( m ) )
        if ( not species or allow_partial or spec_in_block_len == spec_len ) and spec_in_block_len > min_species_per_block:
            maf_writer.write( m )
            maf_blocks_kept += 1
    
    maf_reader.close()
    maf_writer.close()
    
    print "Restricted to species: %s." % ", ".join( species )
    print "%i MAF blocks have been kept." % maf_blocks_kept

if __name__ == "__main__": 
    main()