diff commons/core/writer/TranscriptListWriter.py @ 36:44d5973c188c

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/writer/TranscriptListWriter.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,163 @@
+#
+# 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 SMART.Java.Python.misc.Progress import Progress
+
+class TranscriptListWriter(object):
+    """
+    An interface that writes a transcript list into a file
+    @ivar fileName: name of the file 
+    @type fileName: string
+    @ivar handle: handle to the file
+    @type handle: file handle
+    @ivar header: first lines of the file
+    @type header: string
+    @ivar started: whether some transcripts have already been writted
+    @type started: boolean
+    @ivar lastChromosome: the chromosome on which the transcript which was inserted last
+    @type lastChromosome: string
+    """
+
+
+    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.handle = open(self.fileName, "w")
+        self.started = False
+        self.lastChromosome = None
+        self.header = ""
+        self.sequenceFileName = None
+
+
+    def __del__(self):
+        """
+        Destructor
+        """
+        self.close()
+
+
+    def close(self):
+        """
+        Close writer
+        """
+        if self.handle != None and not self.handle.closed:
+            self.handle.close()
+        self.handle = None
+
+
+    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>}
+        """
+        if not self.started:
+            self.handle.write(self.header)
+            self.started = True
+
+        self.handle.write(self.printTranscript(transcript))
+        self.lastChromosome = transcript.getChromosome()
+
+
+    def addElement(self, element):
+        """
+        Same as "addTranscript"
+        @param element: transcript to be written
+        @type    element: class L{Transcript<Transcript>}
+        """
+        self.addTranscript(element)
+
+
+    def addTranscriptList(self, transcriptList):
+        """
+        Add a list of transcripts to the transcripts to be written
+        @param transcriptList: transcripts to be written
+        @type    transcriptList: class L{TranscriptList<TranscriptList>}
+        """
+        progress = Progress(transcriptList.getNbTranscripts(), "Writing transcripts", self.verbosity)
+        for transcript in transcriptList.getIterator():
+            self.addTranscript(transcript)
+            progress.inc()
+        progress.done()
+            
+
+    def addTranscriptTable(self, transcriptTable):
+        """
+        Add a list of transcripts in a mySQL table to the transcripts to be written
+        @param transcriptTable: transcripts to be written
+        @type    transcriptTable: class L{MySqlTranscriptTable<MySqlTranscriptTable>}
+        """
+        for transcript in transcriptTable.getIterator():
+            self.addTranscript(transcript)
+            
+            
+    def setTitle(self, title):
+        """
+        Possibly write a title for the list (by default, do nothing)
+        @param title: a title for the list
+        @type title:    string
+        """
+        pass
+    
+    def setFeature(self, feature):
+        """
+        Set the name of the feature
+        @param title: the title of the feature
+        @type    feature: string
+        """
+        pass
+        
+    def setFeaturePart(self, featurePart):
+        """
+        Set the name of the feature part
+        @param title: the title of the feature part
+        @type    featurePart: string
+        """
+        pass
+
+
+    def addSequenceFile(self, fileName):
+        """
+        Get the multi-fasta file of the sequences
+        """
+        self.sequenceFileName = fileName
+        
+        
+    def write(self):
+        """
+        No-op
+        """
+        pass