Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/VarscanHit_v2_2_8.py @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
1 # Copyright INRA (Institut National de la Recherche Agronomique)
2 # http://www.inra.fr
3 # http://urgi.versailles.inra.fr
4 #
5 # This software is governed by the CeCILL license under French law and
6 # abiding by the rules of distribution of free software. You can use,
7 # modify and/ or redistribute the software under the terms of the CeCILL
8 # license as circulated by CEA, CNRS and INRIA at the following URL
9 # "http://www.cecill.info".
10 #
11 # As a counterpart to the access to the source code and rights to copy,
12 # modify and redistribute granted by the license, users are provided only
13 # with a limited warranty and the software's author, the holder of the
14 # economic rights, and the successive licensors have only limited
15 # liability.
16 #
17 # In this respect, the user's attention is drawn to the risks associated
18 # with loading, using, modifying and/or developing or reproducing the
19 # software by the user in light of its specific status of free software,
20 # that may mean that it is complicated to manipulate, and that also
21 # therefore means that it is reserved for developers and experienced
22 # professionals having in-depth computer knowledge. Users are therefore
23 # encouraged to load and test the software's suitability as regards their
24 # requirements in conditions enabling the security of their systems and/or
25 # data to be ensured and, more generally, to use and operate it in the
26 # same conditions as regards security.
27 #
28 # The fact that you are presently reading this means that you have had
29 # knowledge of the CeCILL license and that you accept its terms.
30
31
32 from commons.core.checker.CheckerException import CheckerException
33 from commons.core.parsing.VarscanHit import VarscanHit
34
35 class VarscanHit_v2_2_8(VarscanHit):
36
37 def __init__(self, chrom = "", position = "", ref = "", cns = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = "", mapQualRef = "", mapQualVar = "", readsRefPlus = "", readsRefMinus = "", readsVarPlus = "", readsVarMinus = "", var = ""):
38 self._cns = cns
39 self._mapQualRef = mapQualRef
40 self._mapQualVar = mapQualVar
41 self._readsRefPlus = readsRefPlus
42 self._readsRefMinus = readsRefMinus
43 self._readsVarPlus = readsVarPlus
44 self._readsVarMinus = readsVarMinus
45 VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue)
46
47 ## Equal operator
48 #
49 # @param o a VarscanFileAnalysis instance
50 #
51 def __eq__(self, o):
52 if self._cns == o._cns:
53 return VarscanHit.__eq__(self, o)
54 return False
55
56 def setCns(self, consensus):
57 self._cns = consensus
58
59 def setMapQualRef(self, mapQualRef):
60 self._mapQualRef = mapQualRef
61
62 def setMapQualVar(self, mapQualVar):
63 self._mapQualVar = mapQualVar
64
65 def setReadsRefPlus(self, readsRefPlus):
66 self._readsRefPlus = readsRefPlus
67
68 def setReadsRefMinus(self, readsRefMinus):
69 self._readsRefMinus = readsRefMinus
70
71 def setReadsVarPlus(self, readsVarPlus):
72 self._readsVarPlus = readsVarPlus
73
74 def setReadsVarMinus(self, readsVarMinus):
75 self._readsVarMinus = readsVarMinus
76
77 def getCns(self):
78 return self._cns
79
80 def getMapQualRef(self):
81 return self._mapQualRef
82
83 def getMapQualVar(self):
84 return self._mapQualVar
85
86 def getReadsRefPlus(self):
87 return self._readsRefPlus
88
89 def getReadsRefMinus(self):
90 return self._readsRefMinus
91
92 def getReadsVarPlus(self):
93 return self._readsVarPlus
94
95 def getReadsVarMinus(self):
96 return self._readsVarMinus
97
98 def getHeader(self):
99 return "Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\n"
100
101 def getVarscanLine(self):
102 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\t%s\t%s\t%s\t%s\t%s\t%s\n" % (self.getChrom(), self.getPosition(), self.getRef(), self.getCns(), self.getReadsRef(), self.getReadsVar(), self.getVarFreq(), self.getStrandsRef(), self.getStrandsVar(), self.getQualRef(), self.getQualVar(), self.getPValue(), self.getMapQualRef(), self.getMapQualVar(), self.getReadsRefPlus(), self.getReadsRefMinus(), self.getReadsVarPlus(), self.getReadsVarMinus(), self.getVar())
103
104 def setAttributes(self, lResults, iCurrentLineNumber):
105 if lResults[0] != '':
106 self.setChrom(lResults[0])
107 else:
108 raise CheckerException ("The field Chrom is empty in varscan file in line %s" % iCurrentLineNumber)
109 if lResults[1] != '':
110 self.setPosition(lResults[1])
111 else:
112 raise CheckerException ("The field Position is empty in varscan file in line %s" % iCurrentLineNumber)
113 if lResults[2] != '':
114 self.setRef(lResults[2])
115 else:
116 raise CheckerException ("The field Ref is empty in varscan file in line %s" % iCurrentLineNumber)
117 if lResults[3] != '':
118 self.setCns(lResults[3])
119 else:
120 raise CheckerException ("The field Cons is empty in varscan file in line %s" % iCurrentLineNumber)
121 if lResults[4] != '':
122 self.setReadsRef(lResults[4])
123 if lResults[5] != '':
124 self.setReadsVar(lResults[5])
125 if lResults[6] != '':
126 self.setVarFreq(lResults[6])
127 if lResults[7] != '':
128 self.setStrandsRef(lResults[7])
129 if lResults[8] != '':
130 self.setStrandsVar(lResults[8])
131 if lResults[9] != '':
132 self.setQualRef(lResults[9])
133 if lResults[10] != '':
134 self.setQualVar(lResults[10])
135 if lResults[11] != '':
136 self.setPValue(lResults[11])
137 if lResults[12] != '':
138 self.setMapQualRef(lResults[12])
139 if lResults[13] != '':
140 self.setMapQualVar(lResults[13])
141 if lResults[14] != '':
142 self.setReadsRefPlus(lResults[14])
143 if lResults[15] != '':
144 self.setReadsRefMinus(lResults[15])
145 if lResults[16] != '':
146 self.setReadsVarPlus(lResults[16])
147 if lResults[17] != '':
148 self.setReadsVarMinus(lResults[17])
149 if lResults[18] != '':
150 self.setVar(lResults[18])
151 else:
152 raise CheckerException ("The field varAllele is empty in varscan file in line %s" % iCurrentLineNumber)
153
154 def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
155 varscanString = varscanString.rstrip()
156 lvarscanStringItem = varscanString.split(fieldSeparator)
157 if len(lvarscanStringItem) < 19:
158 raise CheckerException ("This varscan line (l.%s) is not complete" % iCurrentLineNumber)
159 self.setAttributes(lvarscanStringItem, iCurrentLineNumber)
160
161 def convertVarscanHit_v2_2_8_To_VarscanHit(self):
162 iVarscanHit = VarscanHit()
163 iVarscanHit.setChrom(self.getChrom())
164 iVarscanHit.setPosition(self.getPosition())
165 iVarscanHit.setRef(self.getRef())
166 iVarscanHit.setVar(self.getVar())
167 iVarscanHit.setReadsRef(self.getReadsRef())
168 iVarscanHit.setReadsVar(self.getReadsVar())
169 iVarscanHit.setVarFreq(self.getVarFreq())
170 iVarscanHit.setStrandsRef(self.getStrandsRef())
171 iVarscanHit.setStrandsVar(self.getStrandsVar())
172 iVarscanHit.setQualRef(self.getQualRef())
173 iVarscanHit.setQualVar(self.getQualVar())
174 iVarscanHit.setPValue(self.getPValue())
175 return iVarscanHit
176