Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/VarscanHit_v2_2_8_WithTag.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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35:d94018ca4ada | 36:44d5973c188c |
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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 from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8 | |
34 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag | |
35 | |
36 class VarscanHit_v2_2_8_WithTag(VarscanHit_v2_2_8): | |
37 | |
38 def __init__(self, chrom = "", position = "", ref = "", cns = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = "", mapQualRef = "", mapQualVar = "", readsRefPlus = "", readsRefMinus = "", readsVarPlus = "", readsVarMinus = "", var = "", tag = ""): | |
39 self._tag = tag | |
40 VarscanHit_v2_2_8.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue, mapQualRef, mapQualVar, readsRefPlus, readsRefMinus, readsVarPlus, readsVarMinus, var) | |
41 | |
42 def __eq__(self, o): | |
43 if self._tag == o._tag: | |
44 return VarscanHit_v2_2_8.__eq__(self, o) | |
45 return False | |
46 | |
47 def setTag(self, tag): | |
48 self._tag = tag | |
49 | |
50 def getTag(self): | |
51 return self._tag | |
52 | |
53 def getHeader(self): | |
54 return "Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\tTag\n" | |
55 | |
56 def getVarscanLine(self): | |
57 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\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(), self.getTag()) | |
58 | |
59 def setAttributes(self, lResults, iCurrentLineNumber): | |
60 VarscanHit_v2_2_8.setAttributes(self, lResults, iCurrentLineNumber) | |
61 if lResults[19] != '': | |
62 self.setTag(lResults[19]) | |
63 else: | |
64 raise CheckerException ("The field tag is empty in varscan file in line %s" % iCurrentLineNumber) | |
65 | |
66 def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"): | |
67 varscanString = varscanString.rstrip() | |
68 lvarscanStringItem = varscanString.split(fieldSeparator) | |
69 if len(lvarscanStringItem) < 20: | |
70 raise CheckerException ("This varscan line (l.%s) is not complete" % iCurrentLineNumber) | |
71 self.setAttributes(lvarscanStringItem, iCurrentLineNumber) | |
72 | |
73 def convertVarscanHit_v2_2_8_WithTag_To_VarscanHit_WithTag(self): | |
74 iVarscanHit = VarscanHit_WithTag() | |
75 iVarscanHit.setChrom(self.getChrom()) | |
76 iVarscanHit.setPosition(self.getPosition()) | |
77 iVarscanHit.setRef(self.getRef()) | |
78 iVarscanHit.setVar(self.getVar()) | |
79 iVarscanHit.setReadsRef(self.getReadsRef()) | |
80 iVarscanHit.setReadsVar(self.getReadsVar()) | |
81 iVarscanHit.setVarFreq(self.getVarFreq()) | |
82 iVarscanHit.setStrandsRef(self.getStrandsRef()) | |
83 iVarscanHit.setStrandsVar(self.getStrandsVar()) | |
84 iVarscanHit.setQualRef(self.getQualRef()) | |
85 iVarscanHit.setQualVar(self.getQualVar()) | |
86 iVarscanHit.setPValue(self.getPValue()) | |
87 iVarscanHit.setTag(self.getTag()) | |
88 return iVarscanHit |