diff commons/core/parsing/MapperParser.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/MapperParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,129 @@
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# 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 sys
+from SMART.Java.Python.structure.Mapping import Mapping
+
+
+class MapperParser(object):
+    """An interface that parses the output of a generic mapper"""
+
+    def __init__(self, fileName, verbosity = 0):
+        super(MapperParser, self).__init__()
+        self.verbosity = verbosity
+        self.nbMappings = None
+        self.chromosomes = None
+        self.size = None
+        self.currentMapping = Mapping()
+        self.handle = open(fileName)
+        self.currentLineNb = 0
+        self.skipFirstLines()
+        self.fileName = fileName
+        self.startingPoint = self.handle.tell()
+
+
+    def __del__(self):
+        self.handle.close()
+        
+
+    def reset(self):
+        self.handle.seek(self.startingPoint)
+        self.currentLineNb = 0
+
+
+    def getNextMapping(self):
+        for line in self.handle:
+            mapping = self.parseLine(line)
+            self.currentLineNb += 1
+            if mapping != None:
+                return mapping
+        return False
+        
+        
+    def getIterator(self):
+        self.reset()
+        mapping = self.getNextMapping()
+        while mapping:
+            yield mapping
+            mapping = self.getNextMapping()
+                
+                
+    def getInfos(self):
+        self.chromosomes = set()
+        self.nbMappings = 0
+        self.size = 0
+        self.reset()
+        if self.verbosity >= 10:
+            print "Getting information."
+        for mapping in self.getIterator():
+            transcript = mapping.getTranscript()
+            self.chromosomes.add(transcript.getChromosome())
+            self.nbMappings += 1
+            self.size += transcript.getSize()
+            if self.verbosity >= 10 and self.nbMappings % 100000 == 0:
+                sys.stdout.write("    %d mappings read\r" % (self.nbMappings))
+                sys.stdout.flush()
+        self.reset()
+        if self.verbosity >= 10:
+            print "    %d mappings read" % (self.nbMappings)
+            print "Done."
+
+
+    def getNbMappings(self):
+        if self.nbMappings != None:
+            return self.nbMappings
+        self.getInfos()
+        return self.nbMappings
+
+
+    def getNbItems(self):
+        return self.getNbMappings()
+
+
+    def getChromosomes(self):
+        if self.chromosomes != None:
+            return self.chromosomes
+        self.getInfos()
+        return self.chromosomes
+    
+    
+    def getSize(self):
+        if self.size != None:
+            return self.size
+        self.getInfos()
+        return self.size
+    
+    
+    def getNbNucleotides(self):
+        return self.getSize()
+
+
+    def setDefaultTagValue(self, name, value):
+        for mapping in self.getIterator():
+            mapping.setTagValue(name, value)