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

#!/usr/bin/env python

"""
Read a maf and output a multiple block fasta file.
"""
#Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.align import maf
from galaxy.tools.util import maf_utilities

assert sys.version_info[:2] >= ( 2, 4 )

def __main__():
    try:
        maf_reader = maf.Reader( open( sys.argv[1] ) )
    except Exception, e:
        maf_utilities.tool_fail( "Error opening input MAF: %s" % e )
    try:
        file_out = open( sys.argv[2], 'w' )
    except Exception, e:
        maf_utilities.tool_fail( "Error opening file for output: %s" % e )
    try:
        species = maf_utilities.parse_species_option( sys.argv[3] )
        if species:
            num_species = len( species )
        else:
            num_species = 0
    except Exception, e:
        maf_utilities.tool_fail( "Error determining species value: %s" % e )
    try:
        partial = sys.argv[4]
    except Exception, e:
        maf_utilities.tool_fail( "Error determining keep partial value: %s" % e )
    
    if species:
        print "Restricted to species: %s" % ', '.join( species )
    else:
        print "Not restricted to species."
    
    for block_num, block in enumerate( maf_reader ):
        if species:
            block = block.limit_to_species( species )
            if len( maf_utilities.get_species_in_block( block ) ) < num_species and partial == "partial_disallowed": continue
        spec_counts = {}
        for component in block.components:
            spec, chrom = maf_utilities.src_split( component.src )
            if spec not in spec_counts:
                spec_counts[ spec ] = 0
            else:
                spec_counts[ spec ] += 1
            file_out.write( "%s\n" % maf_utilities.get_fasta_header( component, { 'block_index' : block_num, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix = "%s_%i_%i" % ( spec, block_num, spec_counts[ spec ] ) ) )
            file_out.write( "%s\n" % component.text )
        file_out.write( "\n" )
    file_out.close()

if __name__ == "__main__": __main__()