--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/hmmOutput/HmmOutputProcessing.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,39 @@
+import os
+from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
+
+##Concrete implementation for hmmscan and  hmmpfam output methods
+#
+class HmmOutputProcessing (object):
+   
+    ## write a align file from a HmmOutput object
+    #
+    # @param fout handle of align file
+    # @param HmmOutput HmmOutput object in fact a list of hmmOutput containing datas required
+    #        
+    def writeHmmOutputToAlignFile( self, pfamOutput, fout ):    
+        for item in pfamOutput.getList():
+            for i in item:
+                fout.write(i + "\t")
+            fout.write("0\n")
+    
+    ## read an output file from hmm profiles search program and write the corresponding .align file
+    #
+    # @param inputFile file
+    # @param outputFile file
+    #
+    def readHmmOutputsAndWriteAlignFile( self, inputFile, outputFile ):
+        if not os.path.exists(inputFile):
+            print "Warning your input file " + inputFile + " does not exist!\n"
+            return
+        file2parse = open( inputFile )
+        pfamOutput = HmmOutput()
+        if outputFile == "":
+            print "Warning have to specify an output name file!\n"
+            return
+        fout = open(outputFile, "w")        
+        while pfamOutput != None:      
+            pfamOutput = self.readHmmOutput(file2parse)             
+            if pfamOutput != None:  
+                self.writeHmmOutputToAlignFile(pfamOutput, fout)
+        fout.close()
+        file2parse.close()