root/galaxy-central/tools/filters/axt_to_concat_fasta.py @ 2

#!/usr/bin/env python
"""
Adapted from bx/scripts/axt_to_concat_fasta.py
"""
from galaxy import eggs
import pkg_resources
pkg_resources.require( "bx-python" )

import sys
import bx.align.axt

def usage(s=None):
        message = """
axt_to_fasta species1 species2 < axt_file > fasta_file
"""
        if (s == None): sys.exit (message)
        else:           sys.exit ("%s\n%s" % (s,message))


def main():

        # check the command line
        species1 = sys.argv[1]
        species2 = sys.argv[2]

        # convert the alignment blocks

        reader = bx.align.axt.Reader(sys.stdin,support_ids=True,\
                                     species1=species1,species2=species2)
        sp1text = list()
        sp2text = list()
        for a in reader:
                sp1text.append(a.components[0].text)
                sp2text.append(a.components[1].text)
        sp1seq = "".join(sp1text)
        sp2seq = "".join(sp2text)
        print_component_as_fasta(sp1seq,species1)
        print_component_as_fasta(sp2seq,species2)
                


# $$$ this should be moved to a bx.align.fasta module

def print_component_as_fasta(text,src):
        header = ">" + src
        print header
        print text


if __name__ == "__main__": main()