Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/VarscanHit.py @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
parents | 769e306b7933 |
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37:d22fadc825e3 | 38:2c0c0a89fad7 |
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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) |