diff smart_toolShed/commons/core/parsing/BlatToGff.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/parsing/BlatToGff.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,116 @@
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+import optparse
+import os
+from commons.core.parsing.BlatParser import BlatParser
+
+class BlatToGff(object):
+
+
+    def __init__(self):
+        pass
+    
+    def setAttributesFromCmdLine(self):
+        help = '\
+        \nThis Script Launch BlatToGff.\n\n\
+        Example 1: python BlatToGff.py -i blatResultsFile.tab -o outputFile.gff3\n\n'
+        parser = optparse.OptionParser(usage= help, version="CovertSamToFastq.py v1.0")
+        parser.add_option( '-i', '--input', dest='inputBLAT', help='Blat Input File Name [Format: tabular]', default= None )
+        parser.add_option( '-o', '--output', dest='output', help='Output File Name [Format: GFF3]', default= None )
+        parser.add_option( '-n', '--methodname', dest='methodName', help='Method name in col. 3 [Default: None]', default= None )
+        ( options, args ) = parser.parse_args()
+        self._options = options
+    
+    def checkOptions(self):
+        if self._options.inputBLAT == '':
+            raise Exception("ERROR: No Blat file specified for -i !")
+        elif not os.path.exists(self._options.inputBLAT):
+            raise Exception("ERROR: Blat Input File doesn't exist !")
+        else:
+            self._inputFileBlat = self._options.inputBLAT
+            
+        if self._options.output == '':
+            raise Exception("ERROR: No Output file specified for -o !")
+        else:
+            self._outputFileGFF = self._options.output
+            
+        self._methodName = self._options.methodName
+            
+    def run(self):
+        self.checkOptions()
+        self._createGFFOutputFile()
+        BLATFile = open(self._inputFileBlat, 'r')
+        
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        blatLine = BLATFile.readline()
+        numberLine = 6
+        while blatLine != '':
+            gffLine = self.convertBlatObjectToGffLine(blatLine, numberLine)
+            self._printGFFLinesToOutputFile(gffLine)
+            blatLine = BLATFile.readline()
+            numberLine = numberLine + 1
+            
+    def convertBlatObjectToGffLine(self, blatLine, numberLine):
+        iBlatHit = BlatParser()
+        iBlatHit.setAttributesFromString(blatLine, numberLine)
+        col1 = iBlatHit.getTName()
+        col2 = 'BlatToGff'
+        if self._methodName == '' or self._methodName == None:
+            col3 = 'BES'
+        else:
+            col3 = '%s:BES' % self._methodName
+        col4 = iBlatHit.getTStart()
+        col5 = iBlatHit.getTEnd()
+        col6 = '.'
+        col7 = '+'
+        col8 = '.'
+        col9 = 'ID=%s;Name=%s;bes_start=%s;bes_end=%s;bes_size=%s' % (iBlatHit.getQName(), iBlatHit.getQName(), iBlatHit.getTStart(), iBlatHit.getTEnd(), iBlatHit.getTSize())
+        gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9)
+        return gffLine
+    
+    def _createGFFOutputFile(self):
+        GFFfile = open(self._outputFileGFF, 'w')
+        GFFfile.write("##gff-version 3\n")
+        GFFfile.close()
+        
+    def _printGFFLinesToOutputFile(self, line):
+        GFFfile = open(self._outputFileGFF, 'a')
+        GFFfile.write(line)
+        GFFfile.close()
+
+if __name__ == '__main__':
+    iBlatToGff = BlatToGff()
+    iBlatToGff.setAttributesFromCmdLine()
+    iBlatToGff.run()
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