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+ − 1 #
+ − 2 # Copyright INRA-URGI 2009-2011
+ − 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.Mapping import Mapping
+ − 34 from SMART.Java.Python.structure.SubMapping import SubMapping
+ − 35 from SMART.Java.Python.structure.Interval import Interval
+ − 36
+ − 37 class BowtieParser(MapperParser):
+ − 38 """A class that parses BowTie format"""
+ − 39
+ − 40 def __init__(self, fileName, verbosity = 0):
+ − 41 super(BowtieParser, self).__init__(fileName, verbosity)
+ − 42
+ − 43
+ − 44 def __del__(self):
+ − 45 super(BowtieParser, self).__del__()
+ − 46
+ − 47
+ − 48 def getFileFormats():
+ − 49 return ["bowtie"]
+ − 50 getFileFormats = staticmethod(getFileFormats)
+ − 51
+ − 52
+ − 53 def skipFirstLines(self):
+ − 54 pass
+ − 55
+ − 56
+ − 57 def parseLine(self, line):
+ − 58 line = line.strip()
+ − 59 fields = line.split("\t")
+ − 60 if len(fields) not in (7, 8):
+ − 61 raise Exception("Line %d '%s' does not look like a BowTie line (number of fields is %d instead of 7 or 8)" % (self.currentLineNb, line, len(fields)))
+ − 62 name = fields[0]
+ − 63 direction = 1 if fields[1] == "+" else -1
+ − 64 chromosome = fields[2]
+ − 65 genomeStart = int(fields[3]) + 1
+ − 66 sequence = fields[4]
+ − 67 quality = fields[5]
+ − 68 number = int(fields[6])
+ − 69 nbMismatches = 0
+ − 70 if len(fields) == 8:
+ − 71 tags = fields[7]
+ − 72 nbMismatches = len(tags.split(","))
+ − 73
+ − 74 mapping = Mapping()
+ − 75 queryInterval = Interval()
+ − 76 queryInterval.setName(name)
+ − 77 queryInterval.setStart(1)
+ − 78 queryInterval.setEnd(len(sequence) + 1)
+ − 79 targetInterval = Interval()
+ − 80 targetInterval.setChromosome(chromosome)
+ − 81 targetInterval.setStart(genomeStart)
+ − 82 targetInterval.setEnd(genomeStart + len(sequence) - 1)
+ − 83 subMapping = SubMapping()
+ − 84 subMapping.setQueryInterval(queryInterval)
+ − 85 subMapping.setTargetInterval(targetInterval)
+ − 86 mapping.addSubMapping(subMapping)
+ − 87 mapping.setSize(len(sequence))
+ − 88 mapping.setNbMismatches(nbMismatches)
+ − 89 mapping.setDirection(direction)
+ − 90 return mapping
+ − 91
