diff commons/core/writer/TranscriptWriter.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/writer/TranscriptWriter.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,189 @@
+#
+# 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 os
+import sys
+from commons.core.writer.WriterChooser import WriterChooser
+from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
+
+class TranscriptWriter(object):
+    """
+    An interface class that writes a list of transcripts, handle different formats
+    @ivar container: container of the data
+    @type container: L{TranscriptContainer<TranscriptContainer>}
+    @ivar format: format of the data to be printed
+    @type format: string     
+    @ivar file: the file where to print
+    @type file: string 
+    @ivar type: type of the data (transcripts, mappings or mySQL)
+    @type type: string
+    @ivar writer: a transcript list writer
+    @type writer: L{TranscriptListWriter<TranscriptListWriter>} or None
+    @ivar mode: use a container or enter transcript one by one
+    @type mode: string
+    @ivar verbosity: verbosity
+    @type verbosity: int        
+    """
+
+    def __init__(self, file, format, verbosity = 0):
+        """
+        Constructor
+        @param container: container of the data
+        @type container: string
+        @param format: format of the data
+        @type format: string
+        @param file: file where to print
+        @type file: string
+        @param verbosity: verbosity
+        @type verbosity: int
+        """
+        self.container = None
+        self.format = format
+        self.file = file 
+
+        self.verbosity = verbosity
+        self.type = None
+        self.writer = None
+        self.mode = None
+        if self.format == None:
+            sys.exit("Error! Writer input format is empty!")
+
+        if self.format == "sql":
+            self.type = "sql"
+            pos = self.file.rfind(os.sep)
+            if pos > -1:
+                self.file = self.file[pos+1:]
+            self.writer = MySqlTranscriptWriter(self.file, self.verbosity)
+        else:
+            writerChooser = WriterChooser(self.verbosity)
+            writerChooser.findFormat(self.format)
+            self.writer = writerChooser.getWriter(self.file)
+            self.type = writerChooser.getType()
+            
+            
+    def close(self):
+        """
+        Close writer
+        """
+        if self.writer != None:
+            self.writer.close()
+
+
+    def setContainer(self, container):
+        """
+        Set a container for the data
+        @param container: container of the data
+        @type container: class L{TranscriptContainer<TranscriptContainer>}
+        """
+        self.container = container
+        if self.mode == "transcript":
+            raise Exception("Error! TranscriptWriter '%s' on 'transcript' mode is currently used on 'container' mode." % (self.file))
+        self.mode = "container"
+
+
+    def addTranscript(self, transcript):
+        """
+        Add a transcript to write
+        @param transcript: a transcript
+        @type transcript: class L{Transcript<Transcript>}
+        """
+        self.writer.addTranscript(transcript)
+        if self.mode == "container":
+            sys.exit("Error! TranscriptWriter '%s' on 'container' mode is currently used on 'transcript' mode." % (self.file))
+        self.mode = "transcript"
+        
+        
+    def addElement(self, transcript):
+        """
+        Same as addTranscript
+        """
+        self.addTranscript(transcript)
+    
+
+    def setTitle(self, title):
+        """
+        Possibly write a title for the list
+        @param title: a title for the list
+        @type title: string
+        """
+        if self.writer != None:
+            self.writer.setTitle(title)
+
+    def setFeature(self, feature):
+        """
+        Possibly Set the name of the feature
+        @param title: the title of the feature
+        @type    feature: string
+        """
+        if self.writer != None:
+            self.writer.setFeature(feature)
+        
+    def setFeaturePart(self, featurePart):
+        """
+        Possibly Set the name of the feature part
+        @param title: the title of the feature part
+        @type    featurePart: string
+        """
+        if self.writer != None:
+            self.writer.setFeaturePart(featurePart)    
+        
+    def setStrands(self, strands):
+        """
+        Possibly consider both strands separately
+        @param strands: whether both strands should be considered separately
+        @type  strands: boolean
+        """
+        if self.writer != None:
+            self.writer.setStrands(strands)
+            
+        
+    def write(self):
+        """
+        Write the content and possibly convert data
+        """        
+        if self.type == "transcript" or self.type == "sequence":
+            if self.mode == "container":
+                self.writer.addTranscriptList(self.container)
+            return
+
+        if self.mode == "transcript" or self.type == "sequence":
+            self.writer.write()
+            return
+
+        if self.container.format != "sql":
+            self.container.storeIntoDatabase()
+        tables = self.container.getTables()
+        for chromosome in tables:
+            tables[chromosome].rename("%s_%s" % (self.file, chromosome))
+        return
+        
+
+    def addSequenceFile(self, fileName):
+        self.writer.addSequenceFile(fileName)
+            
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