diff commons/tools/replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+
+import re
+from commons.pyRepetUnit.components.AbstractProgramLauncher import AbstractProgramLauncher
+
+class replaceGreaterThanSymbolInFastaHeaderProgramLauncher(AbstractProgramLauncher):
+
+    def __init__( self ):
+        AbstractProgramLauncher.__init__( self )
+        self._formatInFile = "fasta"
+                
+    def run( self ):
+        self.checkInput()
+        fastaHandler = open(self.getInputFile(), "r")
+        lines = fastaHandler.readlines()
+        fastaHandler.close()
+        newFastaName = ".".join([self.getInputFile().split(".")[0], "preprocessed", "fasta"])
+        
+        self._writePreprocessedFastaFile(lines, newFastaName)
+        
+    def _writePreprocessedFastaFile(self, lines, newFastaName):
+        newFastaHandler = open(newFastaName, "w")
+        for line in lines:
+            if re.match(">", line):
+                newLine = re.sub("-->|->", " to ", line)
+                newFastaHandler.write(newLine)
+            else:
+                newFastaHandler.write(line)
+        newFastaHandler.close()
+
+        
+        
+        
+if __name__ == "__main__":
+    i = replaceGreaterThanSymbolInFastaHeaderProgramLauncher()
+    i.checkAttributesFromCmdLine()
+    i.run()