diff commons/launcher/launchTCoffee.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/launchTCoffee.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import getopt
+import 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"] )
+
+from pyRepet.launcher.programLauncher import programLauncher
+
+
+def help():
+    print
+    print "usage: ",sys.argv[0],"[ options ]"
+    print "options:"
+    print "     -h: this help"
+    print "     -i: name of the input file (format='fasta')"
+    print "     -P: parameters"
+    print "     -o: name of the output file (format='aligned fasta', default='inFileName'+fa_aln)"
+    print "     -c: clean"
+    print "     -v: verbosity level (default=0/1)"
+    print
+
+
+def main():
+
+    inFileName = ""
+    parameters = ""
+    outFileName = ""
+    clean = False
+    verbose = 0
+    
+    try:
+        opts, args = getopt.getopt(sys.argv[1:],"hi:P:o: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 == "-P":
+            parameters = a
+        elif o == "-o":
+            outFileName = a
+        elif o == "-c":
+            clean = True
+        elif o == "-v":
+            verbose = "yes"
+            
+    if inFileName == "" and parameters == "":
+        print "ERROR: missing compulsory options"
+        help()
+        sys.exit(1)
+        
+    if outFileName == "":
+        outFileName = "%s.fa_aln" % ( inFileName )
+        
+    if verbose > 0:
+        print "START %s" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+        
+    pL = programLauncher( inFileName )
+    pL.launchTcoffee( outFileName, parameters )
+    
+    if verbose > 0:
+        print "END %s" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+    
+    return 0
+
+
+if __name__ == "__main__":
+    main()