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6
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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 commons.core.parsing.MapperParser import MapperParser
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33 from SMART.Java.Python.structure.Mapping import Mapping
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34
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35
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36 class SeqmapParser(MapperParser):
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37 """A class that parses the output of SeqMap"""
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38
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39 def __init__(self, fileName, verbosity = 0):
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40 super(SeqmapParser, self).__init__(fileName, verbosity)
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41
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42
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43 def __del__(self):
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44 super(SeqmapParser, self).__del__()
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45
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46
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47 def getFileFormats():
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48 return ["seqmap"]
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49 getFileFormats = staticmethod(getFileFormats)
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50
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51
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52 def skipFirstLines(self):
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53 self.startingPoint = self.handle.tell()
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54 self.currentLineNb += 1
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55 if "trans_id" not in self.handle.readline():
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56 self.currentLineNb -= 1
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57 self.handle.seek(self.startingPoint)
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58 self.startingPoint = self.handle.tell()
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59
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60
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61 def parseLine(self, line):
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62 m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\w+)\t+([^\t]+)\t+(\w+)\t+(\d+)\t+([+-])\s*$", line)
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63 if m == None:
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64 sys.exit("\nLine %d '%s' does not have a SeqMap format" % (self.currentLineNb, line))
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65
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66 mapping = Mapping()
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67
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68 mapping.targetInterval.setChromosome(m.group(1))
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69 mapping.targetInterval.setStart(int(m.group(2)))
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70 mapping.targetInterval.setSize(len(m.group(3)))
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71
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72 mapping.queryInterval.setName(m.group(4))
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73 mapping.queryInterval.setStart(1)
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74 mapping.queryInterval.setSize(len(m.group(3)))
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75
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76 mapping.setSize(len(m.group(3)))
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77 mapping.setNbMismatches(int(m.group(6)))
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78 mapping.setDirection(m.group(7))
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79
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80 return mapping
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81
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