diff smart_toolShed/commons/core/writer/SequenceListWriter.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/writer/SequenceListWriter.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,94 @@
+#
+# 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.
+#
+
+class SequenceListWriter(object):
+    """
+    An interface that writes a list of sequences into a file
+    @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.fileName = fileName
+        self.verbosity = verbosity
+        self.handle = open(self.fileName, "w")
+
+
+    def __del__(self):
+        """
+        Destructor
+        """
+        self.close()
+        
+
+    def write(self):
+        """
+        No-op
+        """
+        pass
+        
+        
+    def close(self):
+        """
+        Close writer
+        """
+        if self.handle != None:
+            self.handle.close()
+        
+        
+    def addSequence(self, sequence):
+        """
+        Add a sequence to the list of sequence to be written
+        @param sequence: sequence to be written
+        @type    sequence: class L{Sequence<Sequence>}
+        """
+        self.handle.write(self.getLine(sequence))
+
+
+    def addElement(self, element):
+        """
+        Same as "addSequence"
+        @param element: sequence to be written
+        @type    element: class L{Sequence<Sequence>}
+        """
+        self.addSequence(element)
+