Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/Soap2Parser.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
---|---|
date | Fri, 18 Jan 2013 04:54:14 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/Soap2Parser.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,148 @@ +# +# 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 +