Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/GffParser.py @ 14:c79b9ae3f65f
Deleted selected files
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. # import re import sys from SMART.Java.Python.structure.Interval import Interval from SMART.Java.Python.structure.Transcript import Transcript from commons.core.parsing.TranscriptListParser import TranscriptListParser class GffParser(TranscriptListParser): """A class that parses a GFF file and create a transcript list""" def __init__(self, fileName, verbosity = 0): super(GffParser, self).__init__(fileName, verbosity) def __del__(self): super(GffParser, self).__del__() def getFileFormats(): return ["gff", "gff2", "gff3"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): pass def getInfos(self): self.chromosomes = set() self.nbTranscripts = 0 self.size = 0 self.reset() if self.verbosity >= 10: print "Getting information on %s." % (self.fileName) self.reset() for line in self.handle: line = line.strip() if line == "" or line[0] == "#": continue parts = line.split("\t") if len(parts) != 9: raise Exception("Error! Line '%s' has %d tab-separated fields instead of 9!" % (line, len(parts))) self.chromosomes.add(parts[0]) if parts[8].find("Parent") == -1: self.nbTranscripts += 1 else: self.size += max(int(parts[3]), int(parts[4])) - min(int(parts[3]), int(parts[4])) + 1 if self.verbosity >= 10 and self.nbTranscripts % 100000 == 0: sys.stdout.write(" %d transcripts read\r" % (self.nbTranscripts)) sys.stdout.flush() self.reset() if self.verbosity >= 10: print " %d transcripts read" % (self.nbTranscripts) print "Done." def parseLine(self, line): if not line or line[0] == "#": return None m = re.search(r"^\s*(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+([+-.])\s+(\S+)\s+(\S.*)$", line) if m == None: raise Exception("\nLine %d '%s' does not have a GFF format\n" % (self.currentLineNb, line)) interval = Interval() interval.setChromosome(m.group(1)) interval.setName("unnamed transcript") interval.setStart(min(int(m.group(4)), int(m.group(5)))) interval.setEnd(max(int(m.group(4)), int(m.group(5)))) if m.group(7) == ".": interval.setDirection("+") else: interval.setDirection(m.group(7)) interval.setTagValue("feature", m.group(3)) if m.group(6).isdigit(): interval.setTagValue("score", m.group(6)) remainings = m.group(9).split(";") for remaining in remainings: remaining = remaining.strip() if remaining == "": continue posSpace = remaining.find(" ") posEqual = remaining.find("=") if posEqual != -1 and (posEqual < posSpace or posSpace == -1): parts = remaining.split("=") else: parts = remaining.split() field = parts[0].strip() value = " ".join(parts[1:]).strip(" \"") if field in ("Name", "name", "Sequence", "TE", "SAT"): interval.setName(value) else: try: intValue = int(value) interval.setTagValue(field, intValue) except ValueError: interval.setTagValue(field, value) self.currentTranscriptAddress = self.previousTranscriptAddress if "Parent" in interval.getTagNames(): if self.currentTranscript == None: raise Exception("GFF file does not start with a transcript! First line is '%s'." % (line.strip())) if interval.getTagValue("Parent") != self.currentTranscript.getTagValue("ID"): raise Exception("Exon '%s' is not right after its transcript in GFF file!" % (interval)) self.currentTranscript.addExon(interval) if interval.name == None: interval.name = self.currentTranscript.name return None transcript = self.currentTranscript self.currentTranscript = Transcript() self.currentTranscript.copy(interval) self.previousTranscriptAddress = self.currentAddress if transcript != None and transcript.name.startswith("unnamed"): if "ID" in transcript.getTagNames(): transcript.name = transcript.getTagValue("ID") else: transcript.name = "unnamed transcript %s" % (self.currentLineNb) return transcript