Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/VarscanHit_WithTag.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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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 | |
33 from commons.core.parsing.VarscanHit import VarscanHit | |
34 | |
35 class VarscanHit_WithTag(VarscanHit): | |
36 | |
37 def __init__(self, tag = "", chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""): | |
38 self._tag = tag | |
39 VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue) | |
40 | |
41 def __eq__(self, o): | |
42 if self._tag == o._tag: | |
43 return VarscanHit.__eq__(self, o) | |
44 return False | |
45 | |
46 def setTag(self, tag): | |
47 self._tag = tag | |
48 | |
49 def getTag(self): | |
50 return self._tag | |
51 | |
52 def getHeader(self): | |
53 return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tTag\n" | |
54 | |
55 def getVarscanLine(self): | |
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()) | |
57 | |
58 def setAttributes(self, lResults, iCurrentLineNumber): | |
59 VarscanHit.setAttributes(self, lResults, iCurrentLineNumber) | |
60 if lResults[12] != '': | |
61 self.setTag(lResults[12]) | |
62 | |
63 def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"): | |
64 varscanString = varscanString.rstrip() | |
65 lvarscanStringItem = varscanString.split(fieldSeparator) | |
66 if len(lvarscanStringItem)<13: | |
67 for i in range(len(lvarscanStringItem), 13): | |
68 lvarscanStringItem.append ("") | |
69 self.setAttributes(lvarscanStringItem, iCurrentLineNumber) | |
70 |