Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/PslParser.py @ 27:4e7ee5683ef1
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:30:11 -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 commons.core.parsing.MapperParser import MapperParser from SMART.Java.Python.structure.Mapping import Mapping from SMART.Java.Python.structure.SubMapping import SubMapping from SMART.Java.Python.structure.Interval import Interval from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress class PslParser(MapperParser): """A class that parses the output of PSL format (of SSAHA and BLAT)""" def __init__(self, fileName, verbosity = 0): super(PslParser, self).__init__(fileName, verbosity) def __del__(self): super(PslParser, self).__del__() def getFileFormats(): return ["psl"] getFileFormats = staticmethod(getFileFormats) def getInfos(self): self.chromosomes = set() self.nbMappings = 0 self.size = 0 self.reset() progress = UnlimitedProgress(100000, "Getting info on PSL file, # mappings read:", self.verbosity) for line in self.handle: progress.inc() line = line.strip() if line == "": continue parts = line.split("\t") chromosome = parts[13] self.chromosomes.add(chromosome) self.nbMappings += 1 self.size += len(parts[0]) self.reset() progress.done() def skipFirstLines(self): while "------" not in self.handle.readline(): self.currentLineNb += 1 pass def _computeStarts(self,seqSize,blockSize,start,targetStrand): if targetStrand == "+": pass else: start = seqSize-blockSize-start return start def parseLine(self, line): m = re.search(r"^\s*(psl:\s+)?(\d+)\s+(\d+)\s+(\d+)\s+\d+\s+\d+\s+(\d+)\s+\d+\s+(\d+)\s+([+-]{1,2})\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s*$", line) if m == None: raise Exception("\nLine %d '%s' does not have a PSL format" % (self.currentLineNb, line)) mapping = Mapping() queryStrand = m.group(7)[0] if len(m.group(7)) == 1: targetStrand = "+" else: targetStrand = m.group(7)[1] for i in range(0, int(m.group(16))): size = int(m.group(17).split(",")[i]) queryStart = int(m.group(18).split(",")[i]) targetStart = int(m.group(19).split(",")[i]) querySize = int(m.group(9)) targetSize = int(m.group(13)) subMapping = SubMapping() subMapping.setSize(size) subMapping.setDirection(m.group(7)[0]) queryInterval = Interval() targetInterval = Interval() queryInterval.setName(m.group(8)) queryStart = self._computeStarts(querySize,size,queryStart,targetStrand) queryInterval.setStart(queryStart + 1) queryInterval.setEnd(queryStart + size) queryInterval.setDirection(queryStrand) targetInterval.setChromosome(m.group(12)) targetStart = self._computeStarts(targetSize,size,targetStart,targetStrand) targetInterval.setStart(targetStart + 1) targetInterval.setEnd(targetStart + size) targetInterval.setDirection(targetStrand) subMapping.setQueryInterval(queryInterval) subMapping.setTargetInterval(targetInterval) mapping.addSubMapping(subMapping) mapping.setSize(int(m.group(2)) + int(m.group(3)) + int(m.group(4))) mapping.setNbMismatches(int(m.group(3)) + int(m.group(4))) mapping.setNbGaps(int(m.group(5))) mapping.setDirection(queryStrand) queryInterval = Interval() targetInterval = Interval() queryInterval.setName(m.group(8)) queryInterval.setStart(min(int(m.group(10)), int(m.group(11)))) queryInterval.setEnd( max(int(m.group(10)), int(m.group(11)))) queryInterval.setDirection(queryStrand) targetInterval.setChromosome(m.group(12)) targetInterval.setStart(min(int(m.group(14))+1, int(m.group(15)))) targetInterval.setEnd( max(int(m.group(14))+1, int(m.group(15)))) targetInterval.setDirection(targetStrand) mapping.setQueryInterval(queryInterval) mapping.setTargetInterval(targetInterval) return mapping