Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/Soap2Parser.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 SMART.Java.Python.structure.Mapping import Mapping from SMART.Java.Python.structure.SubMapping import SubMapping from commons.core.parsing.MapperParser import MapperParser def mappingToSubMapping(mapping): subMapping = SubMapping() subMapping.targetInterval.copy(mapping.targetInterval) subMapping.queryInterval.copy(mapping.queryInterval) subMapping.setDirection(mapping.getDirection()) subMapping.size = mapping.size subMapping.tags = mapping.tags return subMapping class Soap2Parser(MapperParser): """A class that parses the output of SOAP2""" def __init__(self, fileName, verbosity = 0): super(Soap2Parser, self).__init__(fileName, verbosity) def __del__(self): super(Soap2Parser, self).__del__() def getFileFormats(): return ["soap2"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): pass def getIterator(self): self.reset() currentName = None currentMappings = [] for line in self.handle: mapping = self.parseLine(line) name = mapping.queryInterval.name if name == currentName: if mapping.getTagValue("end") == "a": currentMappings.append(mapping) else: otherEndMapping = currentMappings.pop(0) newMapping = Mapping() subMappingA = mappingToSubMapping(otherEndMapping) subMappingB = mappingToSubMapping(mapping) subMappingB.queryInterval.setDirection(subMappingA.queryInterval.getDirection()) newMapping.addSubMapping(subMappingA) newMapping.addSubMapping(subMappingB) newMapping.tags = otherEndMapping.tags newMapping.setSize(otherEndMapping.size + mapping.size) newMapping.setNbMismatches(otherEndMapping.getTagValue("nbMismatches") + mapping.getTagValue("nbMismatches")) print otherEndMapping.getTagValue("nbMismatches") print mapping.getTagValue("nbMismatches") print newMapping.getTagValue("nbMismatches") sys.exit() newMapping.setTagValue("qualityString", otherEndMapping.getTagValue("qualityString") + mapping.getTagValue("qualityString")) newMapping.setTagValue("occurrence", "%d" % (newMapping.getTagValue("nbOccurrences") - len(currentMappings))) newMapping.setTagValue("ID", "%s-%s" % (name, newMapping.getTagValue("occurrence"))) del newMapping.tags["end"] yield newMapping else: currentName = mapping.queryInterval.name for currentMapping in currentMappings: yield currentMapping currentMappings = [mapping] self.currentLineNb += 1 def parseLine(self, line): m = re.search(r"^\s*(\S+)\s+(\w+)\s+(\S+)\s+(\d+)\s+([ab])\s+(\d+)\s+([+-])\s+(\w+)\s+(\d+)\s+(\d+)\s+", line) if m == None: sys.exit("\nLine %d '%s' does not have a SOAP2 format" % (self.currentLineNb, line)) name = m.group(1) read = m.group(2) qualityString = m.group(3) nbOccurrences = int(m.group(4)) end = m.group(5) size = int(m.group(6)) direction = m.group(7) chromosome = m.group(8) genomeStart = int(m.group(9)) nbMismatches = int(m.group(10)) mapping = Mapping() if name.endswith("/1") or name.endswith("/2"): name = name[:-2] mapping.queryInterval.name = name mapping.queryInterval.setDirection(direction) mapping.queryInterval.setStart(1) mapping.queryInterval.setEnd(size) mapping.targetInterval.setChromosome(chromosome) mapping.targetInterval.setStart(genomeStart) mapping.targetInterval.setSize(size) mapping.setDirection(direction) mapping.setSize(size) mapping.setNbMismatches(nbMismatches) mapping.setNbGaps(0) mapping.setTagValue("qualityString", qualityString) mapping.setTagValue("nbOccurrences", nbOccurrences) mapping.setTagValue("end", end) return mapping