root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/EGG-INFO/scripts/axt_to_fasta.py

#!/usr/bin/python2.6

"""
Application to convert AXT file to FASTA file. Reads an AXT file from standard 
input and writes a FASTA file to standard out.

usage: %prog < axt_file > fasta_file
"""

__author__ = "Bob Harris (rsharris@bx.psu.edu)"

import sys
import bx.align.axt

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


def main():

        # check the command line

        if (len(sys.argv) > 1):
                usage("give me no arguments")

        # convert the alignment blocks

        reader = bx.align.axt.Reader(sys.stdin,support_ids=True,\
                                     species1="",species2="")

        for a in reader:
                if ("id" in a.attributes): id = a.attributes["id"]
                else:                      id = None
                print_component_as_fasta(a.components[0],id)
                print_component_as_fasta(a.components[1],id)
                print


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

def print_component_as_fasta(c,id=None):
        header = ">%s_%s_%s" % (c.src,c.start,c.start+c.size)
        if (id != None): header += " " + id
        print header
        print c.text


if __name__ == "__main__": main()