--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/launchPhyML.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,87 @@
+#!/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()