diff commons/core/writer/GbWriter.py @ 38:2c0c0a89fad7

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/writer/GbWriter.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,102 @@
+#
+# 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 GbWriter(TranscriptListWriter):
+    """
+    A class that writes a transcript list into a file with GBrowse format
+    @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
+    """
+
+
+    def __init__(self, fileName, verbosity = 0):
+        """
+        Constructor
+        @param fileName: name of the file 
+        @type fileName: string
+        @param verbosity: verbosity
+        @type verbosity: int
+        """
+        self.header = "[READS]\nbgcolor = red\nstrand_arrow = 1\n\n"
+        super(GbWriter, self).__init__(fileName, verbosity)
+     
+        
+    @staticmethod
+    def getFileFormats():
+        """
+        Get the format of the file
+        """
+        return ["gb", "gbrowse"]
+        
+        
+    @staticmethod
+    def getExtension():
+        """
+        Get the usual extension for the file
+        """
+        return "gb"
+        
+        
+    def setColor(self, color):
+        """
+        Set the color of the track
+        @param color: the color of the track
+        @type    color: string
+        """
+        if color != None:
+            self.header = "[READS]\nbgcolor= %s\nstrand_arrow = 1\n\n" % (color)
+        
+        
+    def copyProperties(self, gbParser):
+        """
+        Copy the properties collected by a parser, to produce a similar output
+        @param gbParser: a GBrowse parser
+        @type    gbParser: class L{GbParser<GbParser>}
+        """
+        self.setColor(gbParser.color)
+        
+
+    def printTranscript(self, transcript):
+        """
+        Export the given transcript with GBrowse format
+        Possibly skip the reference if already put
+        @param transcript: transcript to be printed
+        @type transcript: class L{Transcript<Transcript>}
+        @return: a string
+        """
+        if self.lastChromosome != None and self.lastChromosome == transcript.getChromosome():
+            return transcript.printGBrowseLine()
+        return transcript.printGBrowse()