diff smart_toolShed/commons/core/parsing/VarscanFile.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/VarscanFile.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,145 @@
+# 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.
+
+
+from commons.core.parsing.VarscanHit import VarscanHit
+from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag
+from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8
+from commons.core.checker.CheckerException import CheckerException
+from commons.core.parsing.VarscanHit_v2_2_8_WithTag import VarscanHit_v2_2_8_WithTag
+
+class VarscanFile(object):
+
+    def __init__(self, varscanFileName = ""):
+        self._varscanFileName = varscanFileName
+        self._varscanFieldSeparator = "\t"
+        self._lVarscanHits = []
+        self._typeOfVarscanFile = ""
+        
+    def __eq__(self, o):
+        return self._varscanFieldSeparator == o._varscanFieldSeparator and self._lVarscanHits == o._lVarscanHits and self._varscanFileName == o._varscanFileName
+             
+    def setVarscanHitsList(self, lVarscanHits):
+        self._lVarscanHits = lVarscanHits
+    
+    def setHeaderVarcanFile(self, headerVarcanFile):
+        self._headerVarcanFile = headerVarcanFile
+        
+    def setTypeOfVarscanFile(self, type):
+        if type == "Varscan_2_2" or type == "Varscan_2_2_WithTag" or type == "Varscan_2_2_8" or type == "Varscan_2_2_8_WithTag":
+            self._typeOfVarscanFile = type
+        else:
+            self._typeOfVarscanFile = ""
+        
+    def getVarscanHitsList(self):
+        return self._lVarscanHits
+    
+    def getHeaderVarcanFile(self):
+        return self._headerVarcanFile
+    
+    def getListOfVarscanHits(self):
+        return self._lVarscanHits
+    
+    def getTypeOfVarscanFile(self):
+        return self._typeOfVarscanFile
+        
+    def parse(self):
+        varscanFile = open(self._varscanFileName, "r")
+        currentLineNumber = 0
+        line = varscanFile.readline()
+        if "Chrom\tPosition" in line:
+            self.setHeaderVarcanFile(line)
+            line = varscanFile.readline()
+        while line != "":
+            if not "Chrom\tPosition" in line:
+                currentLineNumber += 1
+                line = line.strip()
+                lResults = line.split(self._varscanFieldSeparator)
+                if len(lResults) == 12:
+                    currentVarscanLine = self.createVarscanHit(line, currentLineNumber)
+                    self._typeOfVarscanFile = "Varscan_2_2"
+                elif len(lResults) == 13:
+                    currentVarscanLine = self.createVarscanHitWithTag(line, currentLineNumber)
+                    self._typeOfVarscanFile = "Varscan_2_2_WithTag"
+                elif len(lResults) == 19:
+                    currentVarscanLine = self.createVarscanHit_v2_2_8(line, currentLineNumber)
+                    self._typeOfVarscanFile = "Varscan_2_2_8"
+                elif len(lResults) == 20:
+                    currentVarscanLine = self.createVarscanHit_v2_2_8_WithTag(line, currentLineNumber)
+                    self._typeOfVarscanFile = "Varscan_2_2_8_WithTag"
+                else:
+                    raise CheckerException ("Warning: this line (l.%s) is not a valid varscan line !" % currentLineNumber)
+                self._lVarscanHits.append(currentVarscanLine)
+                line = varscanFile.readline()
+        varscanFile.close()
+        
+    def createVarscanObjectFromLine(self, line, currentLineNumber):
+        if self._typeOfVarscanFile == "Varscan_2_2":
+            VarscanHit =  self.createVarscanHit(line, currentLineNumber)
+            return VarscanHit
+        elif self._typeOfVarscanFile == "Varscan_2_2_WithTag":
+            return self.createVarscanHitWithTag(line, currentLineNumber)
+        elif self._typeOfVarscanFile == "Varscan_2_2_8":
+            return self.createVarscanHit_v2_2_8(line, currentLineNumber)
+        elif self._typeOfVarscanFile == "Varscan_2_2_8_WithTag":
+            return self.createVarscanHit_v2_2_8_WithTag(line, currentLineNumber)
+            
+    def createVarscanHit(self, line, currentLineNumber):
+        iVarscanHit =  VarscanHit()
+        iVarscanHit.setAttributesFromString(line, currentLineNumber)
+        return iVarscanHit
+        
+    def createVarscanHitWithTag(self, line, currentLineNumber):
+        iVarscanHitWithTag =  VarscanHit_WithTag()
+        iVarscanHitWithTag.setAttributesFromString(line, currentLineNumber)
+        return iVarscanHitWithTag
+    
+    def createVarscanHit_v2_2_8(self, line, currentLineNumber):
+        iVarscanHit =  VarscanHit_v2_2_8()
+        iVarscanHit.setAttributesFromString(line, currentLineNumber)
+        return iVarscanHit
+    
+    def createVarscanHit_v2_2_8_WithTag(self, line, currentLineNumber):
+        iVarscanHitWithTag =  VarscanHit_v2_2_8_WithTag()
+        iVarscanHitWithTag.setAttributesFromString(line, currentLineNumber)
+        return iVarscanHitWithTag
+    
+    def selectTypeOfVarscanHitObject(self):
+        if self._typeOfVarscanFile == "":
+            raise CheckerException ("Error: no varscan object found !")
+        elif self._typeOfVarscanFile == "Varscan_2_2":
+            return VarscanHit()
+        elif self._typeOfVarscanFile == "Varscan_2_2_WithTag":
+            return VarscanHit_WithTag()
+        elif self._typeOfVarscanFile == "Varscan_2_2_8":
+            return VarscanHit_v2_2_8()
+        elif self._typeOfVarscanFile == "Varscan_2_2_8_WithTag":
+            return VarscanHit_v2_2_8_WithTag()        
+        
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