|
6
|
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 |
