Mercurial > repos > yufei-luo > s_mart
view commons/core/writer/TranscriptListWriter.py @ 68:85e80c21b1f7 draft
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author | m-zytnicki |
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date | Mon, 16 Nov 2015 12:00:32 -0500 |
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 SMART.Java.Python.misc.Progress import Progress class TranscriptListWriter(object): """ An interface that writes a transcript list 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 @ivar started: whether some transcripts have already been writted @type started: boolean @ivar lastChromosome: the chromosome on which the transcript which was inserted last @type lastChromosome: 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") self.started = False self.lastChromosome = None self.header = "" self.sequenceFileName = None def __del__(self): """ Destructor """ self.close() def close(self): """ Close writer """ if self.handle != None and not self.handle.closed: self.handle.close() self.handle = None 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>} """ if not self.started: self.handle.write(self.header) self.started = True self.handle.write(self.printTranscript(transcript)) self.lastChromosome = transcript.getChromosome() def addElement(self, element): """ Same as "addTranscript" @param element: transcript to be written @type element: class L{Transcript<Transcript>} """ self.addTranscript(element) def addTranscriptList(self, transcriptList): """ Add a list of transcripts to the transcripts to be written @param transcriptList: transcripts to be written @type transcriptList: class L{TranscriptList<TranscriptList>} """ progress = Progress(transcriptList.getNbTranscripts(), "Writing transcripts", self.verbosity) for transcript in transcriptList.getIterator(): self.addTranscript(transcript) progress.inc() progress.done() def addTranscriptTable(self, transcriptTable): """ Add a list of transcripts in a mySQL table to the transcripts to be written @param transcriptTable: transcripts to be written @type transcriptTable: class L{MySqlTranscriptTable<MySqlTranscriptTable>} """ for transcript in transcriptTable.getIterator(): self.addTranscript(transcript) def setTitle(self, title): """ Possibly write a title for the list (by default, do nothing) @param title: a title for the list @type title: string """ pass def setFeature(self, feature): """ Set the name of the feature @param title: the title of the feature @type feature: string """ pass def setFeaturePart(self, featurePart): """ Set the name of the feature part @param title: the title of the feature part @type featurePart: string """ pass def addSequenceFile(self, fileName): """ Get the multi-fasta file of the sequences """ self.sequenceFileName = fileName def write(self): """ No-op """ pass