Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/AxtParser.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 |
children | 94ab73e8a190 |
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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.Mapping import Mapping from SMART.Java.Python.structure.SubMapping import SubMapping from commons.core.parsing.MapperParser import MapperParser from SMART.Java.Python.misc import Utils from SMART.Java.Python.misc.Utils import getHammingDistance class AxtParser(MapperParser): """A class that parses AXT (as given by Mosaik)""" def __init__(self, fileName, verbosity = 0): super(AxtParser, self).__init__(fileName, verbosity) self.queryLine = None self.subjectLine = None def __del__(self): super(AxtParser, self).__del__() def getFileFormats(): return ["axt"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): pass def getInfos(self): self.chromosomes = set() self.nbMappings = 0 self.size = 0 cpt = 0 self.reset() for line in self.handle: line = line.strip() if line == "": continue if cpt % 3 == 0: line = line.strip() parts = line.split(" ") self.chromosomes.add(parts[1]) self.size += int(parts[6]) self.nbMappings += 1 cpt += 1 if self.verbosity >= 10 and self.nbMappings % 100000 == 0: sys.stdout.write(" %d mappings read\r" % (self.nbMappings)) sys.stdout.flush() self.reset() if self.verbosity >= 10: print " %d mappings read" % (self.nbMappings) print "Done." def parseLine(self, line): if line.strip() == "": for line in self.handle: self.currentLineNb += 1 break if line.strip() == "": return None m = re.search(r"^\s*\d+\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+\d+\s*$", line) if m != None: #sys.exit("\nLine %d '%s' does not have an AXT format" % (self.currentLineNb, line)) mapping = Mapping() subMapping = SubMapping() offset = -1 if m.group(7) == "-" else 0 subMapping.queryInterval.setName(m.group(4)) subMapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))-1) subMapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))-1) subMapping.queryInterval.setDirection(m.group(7)) subMapping.targetInterval.setChromosome(m.group(1)) subMapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3))) + offset) subMapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3))) + offset) subMapping.targetInterval.setDirection(1) subMapping.setSize(min(subMapping.targetInterval.getSize(), subMapping.queryInterval.getSize())) subMapping.setDirection(m.group(7)) mapping.addSubMapping(subMapping) mapping.setDirection(m.group(7)) mapping.targetInterval.setChromosome(m.group(1)) mapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3))) + offset) mapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3))) + offset) mapping.queryInterval.setName(m.group(4)) mapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))-1) mapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))-1) mapping.setSize(min(mapping.targetInterval.getSize(), mapping.queryInterval.getSize())) for line in self.handle: string1 = line.strip() self.currentLineNb += 1 break for line in self.handle: string2 = line.strip() self.currentLineNb += 1 break mapping.setNbMismatches(Utils.getHammingDistance(string1, string2)) mapping.setNbGaps(0) self.currentMapping = mapping else: if self.queryLine == None: self.queryLine = line else: self.subjectLine = line seqLen = float(len(self.subjectLine)) dist = float(getHammingDistance(self.queryLine, self.subjectLine)) identity = ((seqLen-dist)/seqLen) *100 self.currentMapping.setIdentity(identity) self.queryLine = None self.subjectLine = None return self.currentMapping