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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.Mapping import Mapping
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33 from commons.core.parsing.MapperParser import MapperParser
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34 from SMART.Java.Python.structure.SubMapping import SubMapping
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35 from SMART.Java.Python.misc import Utils
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36 from SMART.Java.Python.structure.Transcript import Transcript
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37 from commons.core.parsing.TranscriptListParser import TranscriptListParser
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38
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39
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40 class MapParser(TranscriptListParser):
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41 """A class that parses the repet .map files"""
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42
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43 def __init__(self, fileName, verbosity = 0):
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44 self._lineParseRe = re.compile(r"(?P<seqName>\w+)\s(?P<chrName>\w+)\s(?P<sStart>\d+)\s(?P<sEnd>\d+)")
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45 TranscriptListParser.__init__(self, fileName, verbosity)
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46
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47 def getFileFormats():
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48 return ["map"]
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49 getFileFormats = staticmethod(getFileFormats)
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50
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51 def skipFirstLines(self):
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52 return
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53
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54 def parseLine(self, line):
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55 m = self._lineParseRe.search(line)
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56
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57 if m == None:
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58 sys.exit("\nLine %d '%s' does not have a map format" % (self.currentLineNb, line))
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59
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60 transcript = Transcript()
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61 transcript.setChromosome(m.group("chrName"))
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62 transcript.setStart(min(int(m.group("sStart")), int(m.group("sEnd"))))
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63 transcript.setEnd(max(int(m.group("sStart")), int(m.group("sEnd"))))
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64 transcript.setName(m.group("seqName"))
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65 transcript.setDirection(1)
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66
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67 return transcript
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