Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/AxtParser.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/AxtParser.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,140 @@ +# +# 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: + mapping = Mapping() + subMapping = SubMapping() + + subMapping.queryInterval.setName(m.group(4)) + subMapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))) + subMapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))) + subMapping.queryInterval.setDirection(m.group(7)) + + subMapping.targetInterval.setChromosome(m.group(1)) + subMapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3)))) + subMapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3)))) + 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)))) + mapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3)))) + + mapping.queryInterval.setName(m.group(4)) + mapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))) + mapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))) + + mapping.setSize(min(mapping.targetInterval.getSize(), mapping.queryInterval.getSize())) + + self.currentMapping = mapping + return None + if self.queryLine == None: + self.queryLine = line + return None + self.subjectLine = line + seqLen = float(len(self.subjectLine)) + dist = float(getHammingDistance(self.queryLine, self.subjectLine)) + self.currentMapping.setNbMismatches(getHammingDistance(self.queryLine, self.subjectLine)) + self.currentMapping.setNbGaps(0) + self.queryLine = None + self.subjectLine = None + return self.currentMapping + + +