--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/hmmOutput/HmmscanOutputProcessing.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,36 @@
+import re
+from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
+from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing
+    
+##Concrete implementation for hmmscan output specific methods
+#
+class HmmscanOutputProcessing (HmmOutputProcessing):
+    
+    ## read an hmmscan output from a file, return a array with results useful to build a .align file
+    #    
+    # @param file handle of file generated by software searching hmm profiles
+    #
+    def readHmmOutput( self, hmmerOutputFile ):
+        #Tested with HMMER 3 on Linux
+        line = hmmerOutputFile.readline()
+        tabResult = None
+        if (line == ""):            
+            tabResult = None
+            return tabResult
+        tabResult = HmmOutput()
+        
+        while line != "":
+            line = hmmerOutputFile.readline()
+            if not(re.match("^#.*$", line)) and line != "":            
+                lLines = re.split("\s+", line)
+                seqName = lLines[3]
+                profilName = lLines[0]
+                iValue = lLines[12]
+                score =  lLines[13]
+                queryCoordStart =lLines[17]
+                queryCoordEnd = lLines[18]
+                subjectCoordStart = lLines[15]
+                subjectCoordEnd = lLines[16]
+                tabResult.append([seqName, queryCoordStart, queryCoordEnd, profilName, subjectCoordStart, subjectCoordEnd, iValue, score]) 
+        return tabResult
+