Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/VarscanHit_WithTag.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
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