diff commons/pyRepetUnit/fastaTranslation/allFrames/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/fastaTranslation/allFrames/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,88 @@
+#!/usr/bin/env python
+
+from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX
+from commons.core.utils.FileUtils import FileUtils
+import os
+import sys
+import getopt
+
+#------------------------------------------------------------------------------
+
+def help():
+
+    """
+    Give the command-line parameters.
+    """
+
+    print ""
+    print "usage: ",sys.argv[0],"[ options ]"
+    print "options:"
+    print "     -h: this help"
+    print "     -i: name of the nucleotidic input file (format='fasta')"
+    print "     -o: name of the output file (default=inFileName+'_aa')"
+    print "     -v: verbose (default=0/1/2)"
+    print "     -c: clean"
+    print ""
+
+#------------------------------------------------------------------------------
+
+def main():
+
+    inFileName = ""
+    outFileName = ""
+    verbose = 0
+    clean = False
+
+    try:
+        opts = getopt.getopt(sys.argv[1:],"hi:o:v:c")[0]
+    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 == "-v":
+            verbose = int(a)
+        elif o == "-c":
+            clean = True
+            
+    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 outFileName == "":
+        outFileName = "%s_aa" % ( inFileName )
+    
+    iTIAFARSBX = TranslateInAllFramesAndReplaceStopByX()
+    iTIAFARSBX.setInputFile( inFileName )
+    iTIAFARSBX.setOutputFile( outFileName )
+    iTIAFARSBX.run( )
+    
+    if clean == True:
+        os.remove( inFileName )
+
+    if verbose > 0:
+        if FileUtils.isRessourceExists( outFileName ) and not(FileUtils.isEmpty( outFileName )):
+            print "%s finished successfully" % (sys.argv[0].split("/")[-1])
+            sys.stdout.flush()
+        else:
+            print "warning %s execution failed" % (sys.argv[0].split("/")[-1])
+            sys.stdout.flush()
+
+    return 0
+
+#------------------------------------------------------------------------------
+
+if __name__ == '__main__':
+    main()
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