diff smart_toolShed/commons/core/writer/EmblWriter.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/writer/EmblWriter.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,116 @@
+#
+# 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.
+#
+from commons.core.writer.TranscriptListWriter import TranscriptListWriter
+
+
+class EmblWriter(TranscriptListWriter):
+    """
+    A class that writes a transcript list into several files with EMBL format
+    @ivar fileName: name of the file 
+    @type fileName: string
+    @ivar handle: handle to the file
+    @type handle: file handle
+    """
+
+
+    def __init__(self, fileName, verbosity = 0):
+        """
+        Constructor
+        @param fileName: name of the file 
+        @type fileName: string
+        @param verbosity: verbosity
+        @type verbosity: int
+        """
+        self.fileName = fileName
+        self.verbosity = verbosity
+        self.handles = {}
+        self.handle = None
+
+
+    def __del__(self):
+        """
+        Destructor
+        Trick to append the sequences at the end of the EMBL files
+        """
+        handle                = open(self.sequenceFileName)
+        currentHandle = None
+        for line in handle:
+            if line[0] == ">":
+                chromosome = line[1:].strip()
+                if chromosome in self.handles:
+                    currentHandle = self.handles[chromosome]
+                else:
+                    currentHandle = None
+            else:
+                if currentHandle != None:
+                    currentHandle.write(line)
+        handle.close()
+        for handle in self.handles.values():
+            handle.close()
+            
+
+    @staticmethod
+    def getFileFormats():
+        """
+        Get the format of the file
+        """
+        return ["embl"]
+        
+        
+    @staticmethod
+    def getExtension():
+        """
+        Get the usual extension for the file
+        """
+        return "embl"
+
+
+    def addTranscript(self, transcript):
+        """
+        Add a transcript to the list of transcripts to be written
+        @param transcript: transcript to be written
+        @type    transcript: class L{Transcript<Transcript>}
+        """
+        chromosome = transcript.getChromosome()
+        if chromosome not in self.handles:
+            self.handles[chromosome] = open("%s%s.embl" % (self.fileName[:-len(".embl")], chromosome.title()), "w")
+        self.handles[chromosome].write(self.printTranscript(transcript))
+
+
+    def printTranscript(self, transcript):
+        """
+        Export the given transcript with GFF2 format
+        @param transcript: transcript to be printed
+        @type transcript: class L{Transcript<Transcript>}
+        @return: a string
+        """
+        return transcript.printEmbl()
+
+