diff smart_toolShed/commons/core/parsing/TranscriptListParser.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/TranscriptListParser.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,182 @@
+#
+# 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.TranscriptList import TranscriptList
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+
+class TranscriptListParser(object):
+    """A (quite generic) class that reads a list of transcripts"""
+
+    def __init__(self, fileName, verbosity = 0):
+        self.verbosity         = verbosity
+        self.fileName          = fileName
+        self.nbTranscripts     = None
+        self.size              = None
+        self.chromosomes       = None
+        self.currentTranscript = None
+        self.currentLineNb     = 0
+        self.previousTranscriptAddress = None
+        try:
+            self.handle = open(self.fileName)
+        except IOError:
+            raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName))
+        self.skipFirstLines()
+
+
+    def __del__(self):
+        self.close()
+        
+
+    def getFileFormats():
+        pass
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def close(self):
+        if self.handle != None and not self.handle.close:
+            self.handle.close()
+        self.handle = None
+
+
+    def reset(self):
+        self.handle.seek(0)
+        self.skipFirstLines()
+        self.currentTranscript = None
+        self.currentLineNb     = 0
+        self.currentTranscriptAddress  = self.handle.tell()
+        self.currentAddress            = self.handle.tell()
+
+
+    def gotoAddress(self, address):
+        self.reset()
+        self.handle.seek(address)
+        self.currentTranscriptAddress = address
+        self.currentAddress           = address
+                
+        
+    def parse(self):
+        transcriptList = TranscriptList()
+        progress = Progress(self.getNbTranscripts(), "Reading %s" % (self.fileName), self.verbosity)
+        for line in self.handle:
+            self.currentLineNb += 1
+            transcript = self.parseLine(line)
+            transcriptList.addTranscript(transcript)
+            progress.inc()
+        progress.done()
+        return transcriptList
+
+
+    def getIterator(self):
+        self.reset()
+        transcript = self.getNextTranscript()
+        while transcript != None:
+            yield transcript
+            transcript = self.getNextTranscript()
+
+
+    def getCurrentAddress(self):
+        return self.currentAddress
+
+
+    def getCurrentTranscriptAddress(self):
+        return self.currentTranscriptAddress
+
+
+    def getNextTranscript(self):
+        self.currentAddress = self.handle.tell()
+        line = self.handle.readline()
+        while line != "":
+            line = line.strip()
+            self.currentLineNb += 1
+            transcript = self.parseLine(line)
+            if transcript != None:
+                return transcript
+            self.currentAddress = self.handle.tell()
+            line = self.handle.readline()
+        transcript = self.currentTranscript
+        self.currentTranscriptAddress = self.previousTranscriptAddress
+        self.currentTranscript = None
+        return transcript
+
+
+    def getInfos(self):
+        self.chromosomes = set()
+        self.nbTranscripts = 0
+        self.size = 0
+        self.reset()
+        progress = UnlimitedProgress(100000, "Getting information on %s." % (self.fileName), self.verbosity-9)
+        transcript = self.getNextTranscript()
+        for transcript in self.getIterator():
+            self.chromosomes.add(transcript.getChromosome())
+            self.nbTranscripts += 1
+            self.size += transcript.getSize()
+            progress.inc()
+        progress.done()
+        self.reset()
+
+    
+    def getNbTranscripts(self):
+        if self.nbTranscripts != None:
+            return self.nbTranscripts
+        self.getInfos()
+        return self.nbTranscripts
+
+
+    def getNbItems(self):
+        return self.getNbTranscripts()
+
+
+    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 transcript in self.getIterator():
+            transcript.setTag(name, value)
+            
+    def __eq__(self, o):
+        if o == None:
+            return False
+        return self.fileName == o.fileName and self.nbTranscripts == o.nbTranscripts and self.size == o.size and self.chromosomes == o.chromosomes