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