Mercurial > repos > yufei-luo > s_mart
diff commons/core/writer/TranscriptListWriter.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/TranscriptListWriter.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,163 @@ +# +# 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