Mercurial > repos > yufei-luo > s_mart
view commons/core/writer/Gff3Writer.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -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 Gff3Writer(TranscriptListWriter): """ A class that writes a transcript list into a file with GFF3 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, title="S-MART", feature="transcript", featurePart="exon"): """ Constructor @param fileName: name of the file @type fileName: string @param verbosity: verbosity @type verbosity: int """ self.header = "" self.title = title self.feature = feature self.featurePart = featurePart super(Gff3Writer, self).__init__(fileName, verbosity) @staticmethod def getFileFormats(): """ Get the format of the file """ return ["gff3", "gff"] @staticmethod def getExtension(): """ Get the usual extension for the file """ return "gff3" def setTitle(self, title): """ Set the title of the transcripts @param title: the title of the transcripts @type title: string """ self.title = title def setFeature(self, feature): """ Set the name of the feature @param title: the title of the feature @type feature: string """ self.feature = feature def setFeaturePart(self, featurePart): """ Set the name of the feature part @param title: the title of the feature part @type featurePart: string """ self.featurePart = featurePart 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 """ direction = "+" if transcript.getDirection() == -1: direction = "-" transcript.sortExonsIncreasing() if "ID" not in transcript.getTagValues(): transcript.setTagValue("ID", transcript.getUniqueName()) feature = self.feature tags = transcript.tags if "feature" in transcript.getTagNames(): feature = transcript.getTagValue("feature") del transcript.tags["feature"] score = "." if "score" in transcript.getTagNames(): score = "%d" % (int(transcript.getTagValue("score"))) del transcript.tags["score"] comment = transcript.getTagValues(";", "=") string = "%s\t%s\t%s\t%d\t%d\t%s\t%s\t.\t%s\n" % (transcript.getChromosome(), self.title, feature, transcript.getStart(), transcript.getEnd(), score, direction, comment) if len(transcript.exons) > 1: for i, exon in enumerate(transcript.getExons()): if "score" in exon.getTagNames(): score = "%d" % (int(exon.getTagValue("score"))) string += "%s\t%s\t%s\t%d\t%d\t%s\t%s\t.\tID=%s-%s%d;Name=%s-%s%d;Parent=%s\n" % (transcript.getChromosome(), self.title,self.featurePart, exon.getStart(), exon.getEnd(), score, direction, transcript.getTagValue("ID"),self.featurePart, i+1, transcript.name,self.featurePart, i+1, transcript.getTagValue("ID")) self.tags = tags return string