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

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#!/usr/bin/env python

import os
import sys
import getopt

from pyRepet.launcher.programLauncher import programLauncher
from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders


def help():
    print
    print "usage: ",sys.argv[0],"[ options ]"
    print "options:"
    print "     -h: this help"
    print "     -i: name of the input file (aligned fasta)"
    print "     -c: clean"
    print "     -v: verbose (default=0)"
    print
    
    
def main():
    
    inFileName = ""
    clean = False
    verbose = 0
    try:
        opts,args=getopt.getopt(sys.argv[1:],"hi: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 == "-c":
            clean = True
        elif o == "-v":
            verbose = int(a)
    if inFileName == "":
        print "ERROR: missing compulsory options"
        help(); sys.exit(1)

    if verbose > 0:
        print "START %s" % (sys.argv[0].split("/")[-1])
        sys.stdout.flush()
        
    csh = ChangeSequenceHeaders()
    csh.setInputFile( inFileName )
    csh.setFormat( "fasta" )
    csh.setStep( 1 )
    csh.setPrefix( "seq" )
    csh.setLinkFile( inFileName+".shortHlink" )
    csh.setOutputFile( inFileName+".shortH" )
    csh.run()
    
    pL = programLauncher( inFileName+".shortH" )
    
    pL.launchSreformat( outFormat="phylip", outFileName=inFileName+".shortH.phylip", verbose=verbose )
    
    pL.reset( inFileName+".shortH.phylip" )
    
    pL.launchPhyML( verbose=verbose )
    
    csh.setInputFile( inFileName+".shortH.phylip_phyml_tree.txt" )
    csh.setFormat( "newick" )
    csh.setStep( 2 )
    csh.setLinkFile( inFileName+".shortHlink" )
    csh.setOutputFile( inFileName+"_phyml.newick" )
    csh.run()
    
    if clean:
        for f in [ inFileName+".shortH", inFileName+".shortHlink", inFileName+".shortH.phylip",
                   inFileName+".shortH.phylip_phyml_lk.txt", inFileName+".shortH.phylip_phyml_tree.txt" ]:
            os.remove( f )
        os.system( "mv %s.shortH.phylip_phyml_stat.txt %s_phyml.txt" % ( inFileName, inFileName ) )

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

    return 0


if __name__ == "__main__":
    main()