--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/launchMafft.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,104 @@
+#!/usr/bin/env python
+
+# DEPRECATED
+
+import user, os, sys, getopt, exceptions
+
+if not os.environ.has_key( "REPET_PATH" ):
+    print "*** Error: no environment variable REPET_PATH"
+    sys.exit(1)
+sys.path.append( os.environ["REPET_PATH"] )
+
+import pyRepet.launcher.programLauncher
+import pyRepet.seq.fastaDB
+from pyRepet.seq.BioseqDB import *
+
+#------------------------------------------------------------------------------
+
+def help():
+
+    print
+    print "DEPRECATED"
+    print
+    print "usage: ",sys.argv[0],"[ options ]"
+    print "options:"
+    print "     -h: this help"
+    print "     -i: name of the input file (format='fasta')"
+    print "     -o: name of the output file (default=inFileName+'.fa_aln')"
+    print "     -v: verbose (default=0/1)"
+    print
+
+#------------------------------------------------------------------------------
+
+def main():
+    
+    """
+    This program launches MAFFT to build a multiple sequence alignment.
+    """
+
+    inFileName = ""
+    outFileName = ""
+    verbose = 0
+    
+    try:
+        opts,args=getopt.getopt(sys.argv[1:],"hi:o:v:")
+    except getopt.GetoptError:
+        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 == "-v":
+            verbose = int(a)
+            
+    if inFileName == "":
+        print "*** Error: missing compulsory options"
+        help()
+        sys.exit(1)
+        
+    if verbose > 0:
+        print "beginning of %s" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+        
+    if verbose > 0:
+        print "build a multiple alignment from '%s'..." % ( inFileName )
+        sys.stdout.flush()
+        
+    pyRepet.seq.fastaDB.shortenSeqHeaders( inFileName )
+    
+    bsDB = BioseqDB( inFileName+".shortH" )
+    bsDB.upCase()
+    bsDB.save( inFileName+".shortHtmp" )
+    del bsDB
+    os.rename( inFileName+".shortHtmp", inFileName+".shortH" )
+    
+    pL = pyRepet.launcher.programLauncher.programLauncher( inFileName+".shortH" )
+    pL.launchMafft( outFileName=inFileName+".shortH.fa_aln", verbose=verbose )
+    
+    pyRepet.seq.fastaDB.retrieveInitSeqHeaders( inFileName+".shortH.fa_aln",
+                                                inFileName+".shortHlink",
+                                                inFileName+".shortH.fa_aln.initH",
+                                                verbose-1 )
+    
+    if outFileName == "":
+        outFileName = "%s.fa_aln" % ( inFileName )
+    os.system( "mv %s.shortH.fa_aln.initH %s" % ( inFileName, outFileName ) )
+    
+    for f in [inFileName+".shortH",inFileName+".shortH.fa_aln",inFileName+".shortHlink"]:
+        os.remove( f )
+        
+    if verbose > 0:
+        print "%s finished successfully" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+        
+    return 0
+
+#------------------------------------------------------------------------------
+
+if __name__ == '__main__':
+    main()