Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/commons/core/writer/SequenceListWriter.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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--- /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) +