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

#!/usr/bin/env python

"""
Read a maf and output a single block fasta file, concatenating blocks

usage %prog species1,species2 maf_file out_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:
        species = maf_utilities.parse_species_option( sys.argv[1] )
    except Exception, e:
        maf_utilities.tool_fail( "Error determining species value: %s" % e )
    try:
        input_filename = sys.argv[2]
    except Exception, e:
        maf_utilities.tool_fail( "Error reading MAF filename: %s" % e )
    try:
        file_out = open( sys.argv[3], 'w' )
    except Exception, e:
        maf_utilities.tool_fail( "Error opening file for output: %s" % e )
    
    if species:
        print "Restricted to species: %s" % ', '.join( species )
    else:
        print "Not restricted to species."
    
    if not species:
        try:
            species = maf_utilities.get_species_in_maf( input_filename )
        except Exception, e:
            maf_utilities.tool_fail( "Error determining species in input MAF: %s" % e )
    
    for spec in species:
        file_out.write( ">" + spec + "\n" )
        try:
            for start_block in maf.Reader( open( input_filename, 'r' ) ):
                for block in maf_utilities.iter_blocks_split_by_species( start_block ):
                    block.remove_all_gap_columns() #remove extra gaps
                    component = block.get_component_by_src_start( spec ) #blocks only have one occurrence of a particular species, so this is safe
                    if component:
                        file_out.write( component.text )
                    else:
                        file_out.write( "-" * block.text_size )
        except Exception, e:
            maf_utilities.tool_fail( "Your MAF file appears to be malformed: %s" % e )
        file_out.write( "\n" )
    file_out.close()


if __name__ == "__main__": __main__()