Mercurial > repos > yufei-luo > s_mart
view commons/core/writer/EmblWriter.py @ 30:5677346472b5
Deleted selected files
author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:45:52 -0400 |
parents | 769e306b7933 |
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# # 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()