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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/writer/FastaWriter.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,77 @@
+#
+# 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.SequenceListWriter import SequenceListWriter
+
+
+class FastaWriter(SequenceListWriter):
+    """
+    A class that writes a sequence list into a file with FASTA 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
+        """
+        super(FastaWriter, self).__init__(fileName, verbosity)
+
+    @staticmethod
+    def getFileFormats():
+        """
+        Get the format of the file
+        """
+        return ["fasta", "mfa"]
+
+
+    @staticmethod
+    def getExtension():
+        """
+        Get the usual extension for the file
+        """
+        return "fasta"
+        
+        
+    def getLine(self, sequence):
+        """
+        Convert a sequence
+        @param sequence: sequence to be written
+        @type    sequence: class L{Sequence<Sequence>}
+        """
+        return sequence.printFasta()