--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/writer/SamWriter.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,101 @@
+#
+# 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 random
+from commons.core.writer.TranscriptListWriter import TranscriptListWriter
+
+
+class SamWriter(TranscriptListWriter):
+    """
+    A class that writes a transcript list into a file with SAM format
+    @ivar sizes: estimated sizes of the chromosomes
+    @type sizes: dict of string to int
+    """
+
+
+    def __init__(self, fileName, verbosity = 0):
+        """
+        Constructor
+        @param fileName:    name of the file 
+        @type fileName:     string
+        @param verbosity: verbosity
+        @type verbosity:    int
+        """
+        super(SamWriter, self).__init__(fileName, verbosity)
+        self.sizes         = {}
+        self.headerWritten = False
+        
+        
+    def close(self):
+        """
+        Close file (trick to add header)
+        """
+        super(SamWriter, self).close()
+        if self.headerWritten:
+            return
+        tmpFileName = "tmpFile%d.sam" % (random.randint(0, 100000))
+        tmpHandle = open(tmpFileName, "w")
+        for chromosome, size in self.sizes.iteritems():
+            tmpHandle.write("@SQ\tSN:%s\tLN:%d\n" % (chromosome, size))
+        self.handle = open(self.fileName)
+        for line in self.handle:
+            tmpHandle.write(line)
+        tmpHandle.close()
+        self.handle.close()
+        os.rename(tmpFileName, self.fileName)
+        self.headerWritten = True
+
+
+    @staticmethod
+    def getFileFormats():
+        """
+        Get the format of the file
+        """
+        return ["sam"]
+        
+        
+    @staticmethod
+    def getExtension():
+        """
+        Get the usual extension for the file
+        """
+        return "sam"
+        
+        
+    def printTranscript(self, transcript):
+        """
+        Export the given transcript with GBrowse format
+        @param transcript: transcript to be printed
+        @type transcript: class L{Transcript<Transcript>}
+        @return: a string
+        """
+        self.sizes[transcript.getChromosome()] = max(transcript.getEnd(), self.sizes.get(transcript.getChromosome(), 0))
+        return transcript.printSam()
+