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+ − 1 #
+ − 2 # Copyright INRA-URGI 2009-2010
+ − 3 #
+ − 4 # This software is governed by the CeCILL license under French law and
+ − 5 # abiding by the rules of distribution of free software. You can use,
+ − 6 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 7 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 8 # "http://www.cecill.info".
+ − 9 #
+ − 10 # As a counterpart to the access to the source code and rights to copy,
+ − 11 # modify and redistribute granted by the license, users are provided only
+ − 12 # with a limited warranty and the software's author, the holder of the
+ − 13 # economic rights, and the successive licensors have only limited
+ − 14 # liability.
+ − 15 #
+ − 16 # In this respect, the user's attention is drawn to the risks associated
+ − 17 # with loading, using, modifying and/or developing or reproducing the
+ − 18 # software by the user in light of its specific status of free software,
+ − 19 # that may mean that it is complicated to manipulate, and that also
+ − 20 # therefore means that it is reserved for developers and experienced
+ − 21 # professionals having in-depth computer knowledge. Users are therefore
+ − 22 # encouraged to load and test the software's suitability as regards their
+ − 23 # requirements in conditions enabling the security of their systems and/or
+ − 24 # data to be ensured and, more generally, to use and operate it in the
+ − 25 # same conditions as regards security.
+ − 26 #
+ − 27 # The fact that you are presently reading this means that you have had
+ − 28 # knowledge of the CeCILL license and that you accept its terms.
+ − 29 #
+ − 30 import re
+ − 31 import sys
+ − 32 from commons.core.parsing.MapperParser import MapperParser
+ − 33 from SMART.Java.Python.structure.Interval import Interval
+ − 34 from SMART.Java.Python.structure.SubMapping import SubMapping
+ − 35 from SMART.Java.Python.structure.Mapping import Mapping
+ − 36
+ − 37
+ − 38 class BlastParser(MapperParser):
+ − 39 """A class that parses the output of Blast (-m 8 format)"""
+ − 40
+ − 41 def __init__(self, fileName, verbosity = 0):
+ − 42 super(BlastParser, self).__init__(fileName, verbosity)
+ − 43
+ − 44
+ − 45 def __del__(self):
+ − 46 super(BlastParser, self).__del__()
+ − 47
+ − 48
+ − 49 def getFileFormats():
+ − 50 return ["blast"]
+ − 51 getFileFormats = staticmethod(getFileFormats)
+ − 52
+ − 53
+ − 54 def skipFirstLines(self):
+ − 55 pass
+ − 56
+ − 57
+ − 58 def parseLine(self, line):
+ − 59 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)
+ − 60 if m == None:
+ − 61 sys.exit("\nLine %d '%s' does not have an Blast format" % (self.currentLineNb, line))
+ − 62
+ − 63 mapping = Mapping()
+ − 64
+ − 65 queryInterval = Interval()
+ − 66 queryInterval.setName(m.group(1))
+ − 67 queryInterval.setStart(min(int(m.group(7)), int(m.group(8))))
+ − 68 queryInterval.setEnd(max(int(m.group(7)), int(m.group(8))))
+ − 69
+ − 70 targetInterval = Interval()
+ − 71 targetInterval.setChromosome(m.group(2))
+ − 72 targetInterval.setStart(min(int(m.group(9)), int(m.group(10))))
+ − 73 targetInterval.setEnd(max(int(m.group(9)), int(m.group(10))))
+ − 74
+ − 75 subMapping = SubMapping()
+ − 76 subMapping.setQueryInterval(queryInterval)
+ − 77 subMapping.setTargetInterval(targetInterval)
+ − 78
+ − 79 mapping.addSubMapping(subMapping)
+ − 80
+ − 81 mapping.setIdentity(round(float(m.group(3))))
+ − 82 mapping.setSize(int(m.group(4)))
+ − 83 mapping.setNbMismatches(int(m.group(5)))
+ − 84 mapping.setNbGaps(int(m.group(6)))
+ − 85 mapping.setDirection((int(m.group(8)) - int(m.group(7))) * (int(m.group(10)) - int(m.group(9))))
+ − 86 mapping.setEvalue(float(m.group(11)))
+ − 87
+ − 88 return mapping