Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/VarscanFileForGnpSNP.py @ 6:769e306b7933
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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 from commons.core.parsing.VarscanHitForGnpSNP import VarscanHitForGnpSNP | |
33 from commons.core.parsing.VarscanFile import VarscanFile | |
34 | |
35 class VarscanFileForGnpSNP(VarscanFile): | |
36 | |
37 def __init__(self, varscanFileName, fastqFileName="", refFastaFileName="", taxonName=""): | |
38 VarscanFile.__init__(self, varscanFileName) | |
39 self._fastqFileName = fastqFileName | |
40 self._refFastaFileName = refFastaFileName | |
41 self._taxonName = taxonName | |
42 self._previousVarscanHit = None | |
43 | |
44 ## Equal operator | |
45 # | |
46 # @param o a VarscanFileAnalysis instance | |
47 # | |
48 def __eq__(self, o): | |
49 return VarscanFile.__eq__(self, o) and self._fastqFileName == o._fastqFileName \ | |
50 and self._refFastaFileName == o._refFastaFileName and self._taxonName == o._taxonName | |
51 | |
52 def getVarscanFieldSeparator(self): | |
53 return self._varscanFieldSeparator | |
54 | |
55 def getFastqFileName(self): | |
56 return self._fastqFileName | |
57 | |
58 def getRefFastaFileName(self): | |
59 return self._refFastaFileName | |
60 | |
61 def getTaxonName(self): | |
62 return self._taxonName | |
63 | |
64 def createVarscanHit(self, line, currentLineNumber): | |
65 line = line.strip() | |
66 lResults = line.split(self._varscanFieldSeparator) | |
67 iVarscanHit = VarscanHitForGnpSNP() | |
68 iVarscanHit.setAttributes(lResults, currentLineNumber) | |
69 iVarscanHit.formatAlleles2GnpSnp() | |
70 iVarscanHit.manageOccurrence(self._previousVarscanHit) | |
71 self._previousVarscanHit = iVarscanHit | |
72 return iVarscanHit |