Mercurial > repos > yufei-luo > s_mart
diff commons/core/writer/FastaWriter.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/writer/FastaWriter.py Fri Jan 18 04:54:14 2013 -0500 @@ -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()