Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/BedParser.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. # import re import sys from SMART.Java.Python.structure.Interval import Interval from commons.core.parsing.TranscriptListParser import TranscriptListParser from SMART.Java.Python.structure.Transcript import Transcript class BedParser(TranscriptListParser): """A class that parses a BED file and create a transcript list""" def __init__(self, fileName, verbosity = 0): self.title = None TranscriptListParser.__init__(self, fileName, verbosity) # def __del__(self): # super(BedParser, self).__del__() def getFileFormats(): return ["bed"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): mark = self.handle.tell() line = self.handle.readline() line = line.strip() m = re.search(r"^\s*track\s+name\s*=\s*(\S+)\s+", line) if m != None: self.title = m.group(1) self.currentLineNb += 1 else: self.handle.seek(mark) return def parseLine(self, line): m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\s*$", line) if m != None: transcript = Transcript() transcript.setChromosome(m.group(1)) transcript.setStart(min(int(m.group(2)), int(m.group(3))-1)) transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1)) transcript.setName("Unnamed") transcript.setDirection(1) return transcript m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\s*$", line) if m != None: transcript = Transcript() transcript.setChromosome(m.group(1)) transcript.setStart(min(int(m.group(2)), int(m.group(3))-1)) transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1)) transcript.setName(m.group(4)) transcript.setDirection(1) return transcript m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\t+\d+\.?\d*\s*$", line) if m != None: transcript = Transcript() transcript.setChromosome(m.group(1)) transcript.setStart(min(int(m.group(2)), int(m.group(3))-1)) transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1)) transcript.setName(m.group(4)) transcript.setDirection(1) return transcript m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\t+\d+\t+([+-])\t+\d+\t+\d+\t+0\t+(\d+)\t+(\S+)\t+(\S+)\s*$", line) if m == None: raise Exception("\nLine %d '%s' does not has a BED format." % (self.currentLineNb, line)) transcript = Transcript() transcript.setChromosome(m.group(1)) transcript.setStart(min(int(m.group(2)), int(m.group(3))-1)) transcript.setEnd(max(int(m.group(2)), int(m.group(3))-1)) transcript.setName(m.group(4)) transcript.setDirection(m.group(5)) nbExons = int(m.group(6)) sizes = m.group(7).split(",") starts = m.group(8).split(",") # check for comment in name m = re.search(r"^([^\(]*)\((\S+)\)$", transcript.getName()) if m != None: transcript.setName(m.group(1)) transcript.setTagValues(m.group(2), ";", "=") # check for nb occurrences in name m = re.search(r"(.*)-(\d+)$", transcript.getName()) if m != None: transcript.setName(m.group(1)) transcript.setOccurrence(int(m.group(2))) for i in range(nbExons): exon = Interval(transcript) exon.setStart(int(starts[i])+transcript.getStart()) exon.setEnd(transcript.getStart()+int(starts[i])+int(sizes[i])-1) exon.setSize(int(sizes[i])) transcript.addExon(exon) if transcript.exons[0].getStart() != transcript.getStart(): sys.exit("There is something wrong with the start of transcript line '%s': transcript starts at %d whereas first exon starts at %d" % (line.strip(), transcript.start, transcript.exons[0].start)) if transcript.exons[-1].getEnd() != transcript.getEnd(): sys.exit("There is something wrong with the end of transcript line '%s': transcript ends at %d whereas last exon ends at %d" % (line.strip(), transcript.end, transcript.exons[-1].end)) return transcript