Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/VarscanFile.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.parsing.VarscanHit import VarscanHit | |
33 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag | |
34 from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8 | |
35 from commons.core.checker.CheckerException import CheckerException | |
36 from commons.core.parsing.VarscanHit_v2_2_8_WithTag import VarscanHit_v2_2_8_WithTag | |
37 | |
38 class VarscanFile(object): | |
39 | |
40 def __init__(self, varscanFileName = ""): | |
41 self._varscanFileName = varscanFileName | |
42 self._varscanFieldSeparator = "\t" | |
43 self._lVarscanHits = [] | |
44 self._typeOfVarscanFile = "" | |
45 | |
46 def __eq__(self, o): | |
47 return self._varscanFieldSeparator == o._varscanFieldSeparator and self._lVarscanHits == o._lVarscanHits and self._varscanFileName == o._varscanFileName | |
48 | |
49 def setVarscanHitsList(self, lVarscanHits): | |
50 self._lVarscanHits = lVarscanHits | |
51 | |
52 def setHeaderVarcanFile(self, headerVarcanFile): | |
53 self._headerVarcanFile = headerVarcanFile | |
54 | |
55 def setTypeOfVarscanFile(self, type): | |
56 if type == "Varscan_2_2" or type == "Varscan_2_2_WithTag" or type == "Varscan_2_2_8" or type == "Varscan_2_2_8_WithTag": | |
57 self._typeOfVarscanFile = type | |
58 else: | |
59 self._typeOfVarscanFile = "" | |
60 | |
61 def getVarscanHitsList(self): | |
62 return self._lVarscanHits | |
63 | |
64 def getHeaderVarcanFile(self): | |
65 return self._headerVarcanFile | |
66 | |
67 def getListOfVarscanHits(self): | |
68 return self._lVarscanHits | |
69 | |
70 def getTypeOfVarscanFile(self): | |
71 return self._typeOfVarscanFile | |
72 | |
73 def parse(self): | |
74 varscanFile = open(self._varscanFileName, "r") | |
75 currentLineNumber = 0 | |
76 line = varscanFile.readline() | |
77 if "Chrom\tPosition" in line: | |
78 self.setHeaderVarcanFile(line) | |
79 line = varscanFile.readline() | |
80 while line != "": | |
81 if not "Chrom\tPosition" in line: | |
82 currentLineNumber += 1 | |
83 line = line.strip() | |
84 lResults = line.split(self._varscanFieldSeparator) | |
85 if len(lResults) == 12: | |
86 currentVarscanLine = self.createVarscanHit(line, currentLineNumber) | |
87 self._typeOfVarscanFile = "Varscan_2_2" | |
88 elif len(lResults) == 13: | |
89 currentVarscanLine = self.createVarscanHitWithTag(line, currentLineNumber) | |
90 self._typeOfVarscanFile = "Varscan_2_2_WithTag" | |
91 elif len(lResults) == 19: | |
92 currentVarscanLine = self.createVarscanHit_v2_2_8(line, currentLineNumber) | |
93 self._typeOfVarscanFile = "Varscan_2_2_8" | |
94 elif len(lResults) == 20: | |
95 currentVarscanLine = self.createVarscanHit_v2_2_8_WithTag(line, currentLineNumber) | |
96 self._typeOfVarscanFile = "Varscan_2_2_8_WithTag" | |
97 else: | |
98 raise CheckerException ("Warning: this line (l.%s) is not a valid varscan line !" % currentLineNumber) | |
99 self._lVarscanHits.append(currentVarscanLine) | |
100 line = varscanFile.readline() | |
101 varscanFile.close() | |
102 | |
103 def createVarscanObjectFromLine(self, line, currentLineNumber): | |
104 if self._typeOfVarscanFile == "Varscan_2_2": | |
105 VarscanHit = self.createVarscanHit(line, currentLineNumber) | |
106 return VarscanHit | |
107 elif self._typeOfVarscanFile == "Varscan_2_2_WithTag": | |
108 return self.createVarscanHitWithTag(line, currentLineNumber) | |
109 elif self._typeOfVarscanFile == "Varscan_2_2_8": | |
110 return self.createVarscanHit_v2_2_8(line, currentLineNumber) | |
111 elif self._typeOfVarscanFile == "Varscan_2_2_8_WithTag": | |
112 return self.createVarscanHit_v2_2_8_WithTag(line, currentLineNumber) | |
113 | |
114 def createVarscanHit(self, line, currentLineNumber): | |
115 iVarscanHit = VarscanHit() | |
116 iVarscanHit.setAttributesFromString(line, currentLineNumber) | |
117 return iVarscanHit | |
118 | |
119 def createVarscanHitWithTag(self, line, currentLineNumber): | |
120 iVarscanHitWithTag = VarscanHit_WithTag() | |
121 iVarscanHitWithTag.setAttributesFromString(line, currentLineNumber) | |
122 return iVarscanHitWithTag | |
123 | |
124 def createVarscanHit_v2_2_8(self, line, currentLineNumber): | |
125 iVarscanHit = VarscanHit_v2_2_8() | |
126 iVarscanHit.setAttributesFromString(line, currentLineNumber) | |
127 return iVarscanHit | |
128 | |
129 def createVarscanHit_v2_2_8_WithTag(self, line, currentLineNumber): | |
130 iVarscanHitWithTag = VarscanHit_v2_2_8_WithTag() | |
131 iVarscanHitWithTag.setAttributesFromString(line, currentLineNumber) | |
132 return iVarscanHitWithTag | |
133 | |
134 def selectTypeOfVarscanHitObject(self): | |
135 if self._typeOfVarscanFile == "": | |
136 raise CheckerException ("Error: no varscan object found !") | |
137 elif self._typeOfVarscanFile == "Varscan_2_2": | |
138 return VarscanHit() | |
139 elif self._typeOfVarscanFile == "Varscan_2_2_WithTag": | |
140 return VarscanHit_WithTag() | |
141 elif self._typeOfVarscanFile == "Varscan_2_2_8": | |
142 return VarscanHit_v2_2_8() | |
143 elif self._typeOfVarscanFile == "Varscan_2_2_8_WithTag": | |
144 return VarscanHit_v2_2_8_WithTag() | |
145 |