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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
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33 from commons.core.parsing.VarscanHit import VarscanHit
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34
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35 class VarscanHit_WithTag(VarscanHit):
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36
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37 def __init__(self, tag = "", chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""):
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38 self._tag = tag
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39 VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue)
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40
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41 def __eq__(self, o):
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42 if self._tag == o._tag:
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43 return VarscanHit.__eq__(self, o)
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44 return False
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45
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46 def setTag(self, tag):
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47 self._tag = tag
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48
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49 def getTag(self):
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50 return self._tag
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51
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52 def getHeader(self):
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53 return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tTag\n"
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54
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55 def getVarscanLine(self):
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56 return "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (self.getChrom(), self.getPosition(), self.getRef(), self.getVar(), self.getReadsRef(), self.getReadsVar(), self.getVarFreq(), self.getStrandsRef(), self.getStrandsVar(), self.getQualRef(), self.getQualVar(), self.getPValue(), self.getTag())
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57
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58 def setAttributes(self, lResults, iCurrentLineNumber):
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59 VarscanHit.setAttributes(self, lResults, iCurrentLineNumber)
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60 if lResults[12] != '':
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61 self.setTag(lResults[12])
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62
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63 def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
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64 varscanString = varscanString.rstrip()
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65 lvarscanStringItem = varscanString.split(fieldSeparator)
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66 if len(lvarscanStringItem)<13:
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67 for i in range(len(lvarscanStringItem), 13):
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68 lvarscanStringItem.append ("")
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69 self.setAttributes(lvarscanStringItem, iCurrentLineNumber)
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70 |