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

#!/usr/bin/python2.6
"""
Application to convert LAV file to MAF file. Reads a LAV file from standard 
input and writes a MAF file to standard out; some statistics are written to 
standard error.

usage: lav_to_maf [--silent] [path=replacement] < lav_file > maf_file
"""

import sys
import copy
import bx.align.lav
import bx.align.maf

def usage(s=None):
        message = __doc__
        if (s == None): sys.exit (message)
        else:           sys.exit ("%s\n%s" % (s,message))


def main():

        # parse the command line

        silent = False
        pathSubs = []

        for arg in sys.argv[1:]:
                if ("=" in arg):
                        ix = arg.find("=")
                        pathSubs.append((arg[:ix],arg[ix+1:]))
                elif (arg == "--silent"):
                        silent = True
                else:
                        usage("unrecognized argument: " + arg)

        # read the alignments and other info

        out = bx.align.maf.Writer(sys.stdout)

        lavsRead = mafsWritten = 0
        for lavBlock in bx.align.lav.Reader(sys.stdin,path_subs=pathSubs):
                lavsRead += 1

                out.write (lavBlock)
                mafsWritten += 1

        if (not silent):
                sys.stderr.write ("%d blocks read, %d written\n" % (lavsRead,mafsWritten))


if __name__ == "__main__": main()