--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/writer/Gff3Writer.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,130 @@
+#
+# 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 Gff3Writer(TranscriptListWriter):
+    """
+    A class that writes a transcript list into a file with GFF3 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, title="S-MART", feature="transcript", featurePart="exon"):
+        """
+        Constructor
+        @param fileName: name of the file 
+        @type fileName: string
+        @param verbosity: verbosity
+        @type verbosity: int
+        """
+        self.header = ""
+        self.title    = title
+        self.feature = feature
+        self.featurePart = featurePart
+        super(Gff3Writer, self).__init__(fileName, verbosity)
+            
+
+    @staticmethod
+    def getFileFormats():
+        """
+        Get the format of the file
+        """
+        return ["gff3", "gff"]
+        
+        
+    @staticmethod
+    def getExtension():
+        """
+        Get the usual extension for the file
+        """
+        return "gff3"
+        
+        
+    def setTitle(self, title):
+        """
+        Set the title of the transcripts
+        @param title: the title of the transcripts
+        @type    title: string
+        """
+        self.title = title
+        
+    def setFeature(self, feature):
+        """
+        Set the name of the feature
+        @param title: the title of the feature
+        @type    feature: string
+        """
+        self.feature = feature
+        
+    def setFeaturePart(self, featurePart):
+        """
+        Set the name of the feature part
+        @param title: the title of the feature part
+        @type    featurePart: string
+        """
+        self.featurePart = featurePart
+
+
+    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
+        """
+        direction = "+"
+        if transcript.getDirection() == -1:
+            direction = "-"
+        transcript.sortExonsIncreasing()
+        if "ID" not in transcript.getTagValues():
+            transcript.setTagValue("ID", transcript.getUniqueName())
+        feature = self.feature
+        tags = transcript.tags
+        if "feature" in transcript.getTagNames():
+            feature = transcript.getTagValue("feature")
+            del transcript.tags["feature"]
+        score = "."
+        if "score" in transcript.getTagNames():
+            score = "%d" % (int(transcript.getTagValue("score")))
+            del transcript.tags["score"]
+        comment = transcript.getTagValues(";", "=")
+        string = "%s\t%s\t%s\t%d\t%d\t%s\t%s\t.\t%s\n" % (transcript.getChromosome(), self.title, feature, transcript.getStart(), transcript.getEnd(), score, direction, comment)
+        if len(transcript.exons) > 1:
+            for i, exon in enumerate(transcript.getExons()):
+                if "score" in exon.getTagNames():
+                    score = "%d" % (int(exon.getTagValue("score")))
+                string += "%s\t%s\t%s\t%d\t%d\t%s\t%s\t.\tID=%s-%s%d;Name=%s-%s%d;Parent=%s\n" % (transcript.getChromosome(), self.title,self.featurePart, exon.getStart(), exon.getEnd(), score, direction, transcript.getTagValue("ID"),self.featurePart, i+1, transcript.name,self.featurePart, i+1, transcript.getTagValue("ID"))
+        self.tags = tags
+        return string
+