Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/commons/core/parsing/VarscanFile.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
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