Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/VarscanHit.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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
34 class VarscanHit(object):
35
36 def __init__(self, chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""):
37 self._chrom = chrom
38 self._position = position
39 self._ref = ref
40 self._var = var
41 self._readsRef = readsRef
42 self._readsVar = readsVar
43 self._varFreq = varFreq
44 self._strandsRef = strandsRef
45 self._strandsVar = strandsVar
46 self._qualRef = qualRef
47 self._qualVar = qualVar
48 self._pValue = pValue
49
50 ## Equal operator
51 #
52 # @param o a VarscanFileAnalysis instance
53 #
54 def __eq__(self, o):
55 return self._chrom == o._chrom and self._position == o._position and self._ref == o._ref and self._var == o._var
56
57 def setChrom(self, chromosome):
58 self._chrom = chromosome
59
60 def setPosition(self, position):
61 self._position = position
62
63 def setRef(self, referenceAllele):
64 self._ref = referenceAllele
65
66 def setVar(self, variantAllele):
67 self._var = variantAllele
68
69 def setReadsRef(self, readsRef):
70 self._readsRef = readsRef
71
72 def setReadsVar(self, readsVar):
73 self._readsVar = readsVar
74
75 def setVarFreq(self, varFreq):
76 self._varFreq = varFreq
77
78 def setStrandsRef(self, strandsRef):
79 self._strandsRef = strandsRef
80
81 def setStrandsVar(self, strandsVar):
82 self._strandsVar = strandsVar
83
84 def setQualRef(self, qualRef):
85 self._qualRef = qualRef
86
87 def setQualVar(self, qualVar):
88 self._qualVar = qualVar
89
90 def setPValue(self, pValue):
91 self._pValue = pValue
92
93 def getChrom(self):
94 return self._chrom
95
96 def getPosition(self):
97 return self._position
98
99 def getRef(self):
100 return self._ref
101
102 def getVar(self):
103 return self._var
104
105 def getReadsRef(self):
106 return self._readsRef
107
108 def getReadsVar(self):
109 return self._readsVar
110
111 def getVarFreq(self):
112 return self._varFreq
113
114 def getStrandsRef(self):
115 return self._strandsRef
116
117 def getStrandsVar(self):
118 return self._strandsVar
119
120 def getQualRef(self):
121 return self._qualRef
122
123 def getQualVar(self):
124 return self._qualVar
125
126 def getPValue(self):
127 return self._pValue
128
129 def getHeader(self):
130 return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n"
131
132 def getVarscanLine(self):
133 return "%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())
134
135 def setAttributes(self, lResults, iCurrentLineNumber):
136 if lResults[0] != '':
137 self.setChrom(lResults[0])
138 else:
139 raise CheckerException ("The field Chrom is empty in varscan file in line %s" % iCurrentLineNumber)
140 if lResults[1] != '':
141 self.setPosition(lResults[1])
142 else:
143 raise CheckerException ("The field Position is empty in varscan file in line %s" % iCurrentLineNumber)
144 if lResults[2] != '':
145 self.setRef(lResults[2])
146 else:
147 raise CheckerException ("The field Ref is empty in varscan file in line %s" % iCurrentLineNumber)
148 if lResults[3] != '':
149 self.setVar(lResults[3])
150 else:
151 raise CheckerException ("The field Var is empty in varscan file in line %s" % iCurrentLineNumber)
152 if lResults[4] != '':
153 self.setReadsRef(lResults[4])
154 if lResults[5] != '':
155 self.setReadsVar(lResults[5])
156 if lResults[6] != '':
157 self.setVarFreq(lResults[6])
158 if lResults[7] != '':
159 self.setStrandsRef(lResults[7])
160 if lResults[8] != '':
161 self.setStrandsVar(lResults[8])
162 if lResults[9] != '':
163 self.setQualRef(lResults[9])
164 if lResults[10] != '':
165 self.setQualVar(lResults[10])
166 if lResults[11] != '':
167 self.setPValue(lResults[11])
168
169 def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
170 varscanString = varscanString.rstrip()
171 lvarscanStringItem = varscanString.split(fieldSeparator)
172 if len(lvarscanStringItem)<12:
173 for i in range(len(lvarscanStringItem), 12):
174 lvarscanStringItem.append ("")
175 self.setAttributes(lvarscanStringItem, iCurrentLineNumber)