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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 from commons.core.parsing.VarscanHitForGnpSNP import VarscanHitForGnpSNP
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33 from commons.core.parsing.VarscanFile import VarscanFile
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34
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35 class VarscanFileForGnpSNP(VarscanFile):
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36
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37 def __init__(self, varscanFileName, fastqFileName="", refFastaFileName="", taxonName=""):
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38 VarscanFile.__init__(self, varscanFileName)
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39 self._fastqFileName = fastqFileName
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40 self._refFastaFileName = refFastaFileName
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41 self._taxonName = taxonName
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42 self._previousVarscanHit = None
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43
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44 ## Equal operator
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45 #
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46 # @param o a VarscanFileAnalysis instance
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47 #
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48 def __eq__(self, o):
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49 return VarscanFile.__eq__(self, o) and self._fastqFileName == o._fastqFileName \
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50 and self._refFastaFileName == o._refFastaFileName and self._taxonName == o._taxonName
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51
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52 def getVarscanFieldSeparator(self):
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53 return self._varscanFieldSeparator
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54
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55 def getFastqFileName(self):
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56 return self._fastqFileName
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57
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58 def getRefFastaFileName(self):
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59 return self._refFastaFileName
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60
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61 def getTaxonName(self):
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62 return self._taxonName
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63
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64 def createVarscanHit(self, line, currentLineNumber):
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65 line = line.strip()
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66 lResults = line.split(self._varscanFieldSeparator)
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67 iVarscanHit = VarscanHitForGnpSNP()
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68 iVarscanHit.setAttributes(lResults, currentLineNumber)
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69 iVarscanHit.formatAlleles2GnpSnp()
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70 iVarscanHit.manageOccurrence(self._previousVarscanHit)
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71 self._previousVarscanHit = iVarscanHit
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72 return iVarscanHit
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