Mercurial > repos > yufei-luo > s_mart
diff commons/core/writer/EmblWriter.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/writer/EmblWriter.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,116 @@ +# +# 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.TranscriptListWriter import TranscriptListWriter + + +class EmblWriter(TranscriptListWriter): + """ + A class that writes a transcript list into several files with EMBL format + @ivar fileName: name of the file + @type fileName: string + @ivar handle: handle to the file + @type handle: file handle + """ + + + 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.handles = {} + self.handle = None + + + def __del__(self): + """ + Destructor + Trick to append the sequences at the end of the EMBL files + """ + handle = open(self.sequenceFileName) + currentHandle = None + for line in handle: + if line[0] == ">": + chromosome = line[1:].strip() + if chromosome in self.handles: + currentHandle = self.handles[chromosome] + else: + currentHandle = None + else: + if currentHandle != None: + currentHandle.write(line) + handle.close() + for handle in self.handles.values(): + handle.close() + + + @staticmethod + def getFileFormats(): + """ + Get the format of the file + """ + return ["embl"] + + + @staticmethod + def getExtension(): + """ + Get the usual extension for the file + """ + return "embl" + + + def addTranscript(self, transcript): + """ + Add a transcript to the list of transcripts to be written + @param transcript: transcript to be written + @type transcript: class L{Transcript<Transcript>} + """ + chromosome = transcript.getChromosome() + if chromosome not in self.handles: + self.handles[chromosome] = open("%s%s.embl" % (self.fileName[:-len(".embl")], chromosome.title()), "w") + self.handles[chromosome].write(self.printTranscript(transcript)) + + + def printTranscript(self, transcript): + """ + Export the given transcript with GFF2 format + @param transcript: transcript to be printed + @type transcript: class L{Transcript<Transcript>} + @return: a string + """ + return transcript.printEmbl() + +