Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/BlastParser.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 |
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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.Interval import Interval from SMART.Java.Python.structure.SubMapping import SubMapping from SMART.Java.Python.structure.Mapping import Mapping class BlastParser(MapperParser): """A class that parses the output of Blast (-m 8 format)""" def __init__(self, fileName, verbosity = 0): super(BlastParser, self).__init__(fileName, verbosity) def __del__(self): super(BlastParser, self).__del__() def getFileFormats(): return ["blast"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): pass def parseLine(self, line): m = re.search(r"^(\S+)\s+(\S+)\s+(\d+\.?\d*)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+([-+]?\d+\.?\d*[eE]?[-+]?\d*)\s+(\d+\.?\d*)\s*$", line) if m == None: sys.exit("\nLine %d '%s' does not have an Blast format" % (self.currentLineNb, line)) mapping = Mapping() queryInterval = Interval() queryInterval.setName(m.group(1)) queryInterval.setStart(min(int(m.group(7)), int(m.group(8)))) queryInterval.setEnd(max(int(m.group(7)), int(m.group(8)))) targetInterval = Interval() targetInterval.setChromosome(m.group(2)) targetInterval.setStart(min(int(m.group(9)), int(m.group(10)))) targetInterval.setEnd(max(int(m.group(9)), int(m.group(10)))) subMapping = SubMapping() subMapping.setQueryInterval(queryInterval) subMapping.setTargetInterval(targetInterval) mapping.addSubMapping(subMapping) mapping.setIdentity(round(float(m.group(3)))) mapping.setSize(int(m.group(4))) mapping.setNbMismatches(int(m.group(5))) mapping.setNbGaps(int(m.group(6))) mapping.setDirection((int(m.group(8)) - int(m.group(7))) * (int(m.group(10)) - int(m.group(9)))) mapping.setEvalue(float(m.group(11))) return mapping