annotate commons/launcher/launchPrank.py @ 18:94ab73e8a190

Uploaded

#!/usr/bin/env python

import os
import sys
import getopt

from pyRepet.launcher.programLauncher import programLauncher


def help():
    print
    print "usage: launchPrank.py [ options ]"
    print "options:"
    print "     -h: this help"
    print "     -i: name of the input file (format=fasta)"
    print "     -o: name of the output file (format=aligned fasta, default='inFileName'+fa_aln)"
    print "     -P: Prank's parameters"
    print "     -c: clean"
    print "     -v: verbose (default=0/1)"
    print


def main():
    """
    Launch PRANK.
    """
    inFileName = ""
    outFileName = ""
    parameters = ""
    clean = False
    verbose = 0

    try:
        opts, args = getopt.getopt( sys.argv[1:], "hi:o:P:cv:" )
    except getopt.GetoptError, err:
        print str(err)
        help()
        sys.exit(1)
    for o,a in opts:
        if o == "-h":
            help()
            sys.exit(0)
        elif o == "-i":
            inFileName = a
        elif o == "-o":
            outFileName = a
        elif o == "-P":
            parameters = a
        elif o == "-c":
            clean = True
        elif o == "-v":
            verbose = int(a)

    if inFileName == "":
        print "ERROR: missing input file (-i)"
        help()
        sys.exit(1)

    if not os.path.exists( inFileName ):
        print "ERROR: can't find file '%s'" % ( inFileName )
        help()
        sys.exit(1)

    if verbose > 0:
        print "START %s" % ( sys.argv[0].split("/")[-1] )
        sys.stdout.flush()

    if outFileName == "":
        outFileName = "%s.fa_aln" % ( inFileName )

    pL = programLauncher( inFileName )
    returnStatus = pL.launchPrank( outFileName, parameters, "yes", verbose )
    if returnStatus != 0:
        print "ERROR: launchPrank() returned '%i'" % ( returnStatus )
        sys.exit(1)

    if verbose > 0:
        print "END %s" % ( sys.argv[0].split("/")[-1] )
        sys.stdout.flush()

    return 0


if __name__ == "__main__":
    main()