Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/commons/core/writer/TranscriptWriter.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/commons/core/writer/TranscriptWriter.py Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,189 @@ +# +# 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. +# +import os +import sys +from commons.core.writer.WriterChooser import WriterChooser +from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter + +class TranscriptWriter(object): + """ + An interface class that writes a list of transcripts, handle different formats + @ivar container: container of the data + @type container: L{TranscriptContainer<TranscriptContainer>} + @ivar format: format of the data to be printed + @type format: string + @ivar file: the file where to print + @type file: string + @ivar type: type of the data (transcripts, mappings or mySQL) + @type type: string + @ivar writer: a transcript list writer + @type writer: L{TranscriptListWriter<TranscriptListWriter>} or None + @ivar mode: use a container or enter transcript one by one + @type mode: string + @ivar verbosity: verbosity + @type verbosity: int + """ + + def __init__(self, file, format, verbosity = 0): + """ + Constructor + @param container: container of the data + @type container: string + @param format: format of the data + @type format: string + @param file: file where to print + @type file: string + @param verbosity: verbosity + @type verbosity: int + """ + self.container = None + self.format = format + self.file = file + + self.verbosity = verbosity + self.type = None + self.writer = None + self.mode = None + if self.format == None: + sys.exit("Error! Writer input format is empty!") + + if self.format == "sql": + self.type = "sql" + pos = self.file.rfind(os.sep) + if pos > -1: + self.file = self.file[pos+1:] + self.writer = MySqlTranscriptWriter(self.file, self.verbosity) + else: + writerChooser = WriterChooser(self.verbosity) + writerChooser.findFormat(self.format) + self.writer = writerChooser.getWriter(self.file) + self.type = writerChooser.getType() + + + def close(self): + """ + Close writer + """ + if self.writer != None: + self.writer.close() + + + def setContainer(self, container): + """ + Set a container for the data + @param container: container of the data + @type container: class L{TranscriptContainer<TranscriptContainer>} + """ + self.container = container + if self.mode == "transcript": + raise Exception("Error! TranscriptWriter '%s' on 'transcript' mode is currently used on 'container' mode." % (self.file)) + self.mode = "container" + + + def addTranscript(self, transcript): + """ + Add a transcript to write + @param transcript: a transcript + @type transcript: class L{Transcript<Transcript>} + """ + self.writer.addTranscript(transcript) + if self.mode == "container": + sys.exit("Error! TranscriptWriter '%s' on 'container' mode is currently used on 'transcript' mode." % (self.file)) + self.mode = "transcript" + + + def addElement(self, transcript): + """ + Same as addTranscript + """ + self.addTranscript(transcript) + + + def setTitle(self, title): + """ + Possibly write a title for the list + @param title: a title for the list + @type title: string + """ + if self.writer != None: + self.writer.setTitle(title) + + def setFeature(self, feature): + """ + Possibly Set the name of the feature + @param title: the title of the feature + @type feature: string + """ + if self.writer != None: + self.writer.setFeature(feature) + + def setFeaturePart(self, featurePart): + """ + Possibly Set the name of the feature part + @param title: the title of the feature part + @type featurePart: string + """ + if self.writer != None: + self.writer.setFeaturePart(featurePart) + + def setStrands(self, strands): + """ + Possibly consider both strands separately + @param strands: whether both strands should be considered separately + @type strands: boolean + """ + if self.writer != None: + self.writer.setStrands(strands) + + + def write(self): + """ + Write the content and possibly convert data + """ + if self.type == "transcript" or self.type == "sequence": + if self.mode == "container": + self.writer.addTranscriptList(self.container) + return + + if self.mode == "transcript" or self.type == "sequence": + self.writer.write() + return + + if self.container.format != "sql": + self.container.storeIntoDatabase() + tables = self.container.getTables() + for chromosome in tables: + tables[chromosome].rename("%s_%s" % (self.file, chromosome)) + return + + + def addSequenceFile(self, fileName): + self.writer.addSequenceFile(fileName) + \ No newline at end of file