Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/CrossSsrAndBesMappedByBlatToGff.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 import os | |
33 import optparse | |
34 from commons.core.parsing.SsrParser import SsrParser | |
35 from commons.core.parsing.BlatParser import BlatParser | |
36 | |
37 class CrossSsrAndBesMappedByBlatToGff(object): | |
38 | |
39 | |
40 def __init__(self): | |
41 self._inputFileSSR = '' | |
42 self._inputFileBlat = '' | |
43 self._outputFileGFF = '' | |
44 | |
45 def setAttributesFromCmdLine(self): | |
46 help = '\ | |
47 \nThis Script Launch CrossSsrAndBesMappedByBlatToGff.\n\n\ | |
48 Example 1: python CrossSsrAndBesMappedByBlatToGff.py -s ssrResultsFile.tab -b blatResultsFile.tab -o outputFile.gff3\n\ | |
49 Example 2: python CrossSsrAndBesMappedByBlatToGff.py -s ssrResultsFile.tab -b blatResultsFile.tab -o outputFile.gff3 -n muscadine:filtre1\n\n' | |
50 | |
51 parser = optparse.OptionParser(usage= help, version="CovertSamToFastq.py v1.0") | |
52 parser.add_option( '-s', '--ssr', dest='inputSSR', help='SSR Input File Name [Format: tabular]', default= None ) | |
53 parser.add_option( '-b', '--blat', dest='inputBLAT', help='Blat Input File Name [Format: tabular]', default= None ) | |
54 parser.add_option( '-o', '--output', dest='output', help='Output File Name [Format: GFF3]', default= None ) | |
55 parser.add_option( '-n', '--methodName', dest='methodName', help='Method name in col. 3 [Default: None]', default= None ) | |
56 ( options, args ) = parser.parse_args() | |
57 self.options = options | |
58 | |
59 def checkOptions(self): | |
60 if self.options.inputSSR == '': | |
61 raise Exception("ERROR: No SSR file specified for -s !") | |
62 elif not os.path.exists(self.options.inputSSR): | |
63 raise Exception("ERROR: SSR Input File doesn't exist !") | |
64 else: | |
65 self._inputFileSSR = self.options.inputSSR | |
66 | |
67 if self.options.inputBLAT == '': | |
68 raise Exception("ERROR: No Blat file specified for -b !") | |
69 elif not os.path.exists(self.options.inputBLAT): | |
70 raise Exception("ERROR: Blat Input File doesn't exist !") | |
71 else: | |
72 self._inputFileBlat = self.options.inputBLAT | |
73 | |
74 if self.options.output == '': | |
75 raise Exception("ERROR: No Output file specified for -o !") | |
76 else: | |
77 self._outputFileGFF = self.options.output | |
78 | |
79 self._methodName = self.options.methodName | |
80 | |
81 def run(self): | |
82 self.checkOptions() | |
83 self._createGFFOutputFile() | |
84 | |
85 dictSsrParser = {} | |
86 dictSsrParser = self.createDictOfSsrParser(dictSsrParser) | |
87 | |
88 BLATFile = open(self._inputFileBlat, 'r') | |
89 | |
90 headerBlatLine = BLATFile.readline() | |
91 headerBlatLine = BLATFile.readline() | |
92 headerBlatLine = BLATFile.readline() | |
93 headerBlatLine = BLATFile.readline() | |
94 headerBlatLine = BLATFile.readline() | |
95 blatLine = BLATFile.readline() | |
96 numberLine = 6 | |
97 while blatLine != '' and blatLine != '\n': | |
98 thisBlatHit = BlatParser() | |
99 thisBlatHit.setAttributesFromString(blatLine, numberLine) | |
100 besName = thisBlatHit.getQName() | |
101 | |
102 if besName in dictSsrParser: | |
103 lLinesToPrint = self.createListOfGFFLinesForThisBesWithSSR(thisBlatHit, dictSsrParser) | |
104 self._printGFFLinesToOutputFile(lLinesToPrint) | |
105 | |
106 blatLine = BLATFile.readline() | |
107 numberLine = numberLine + 1 | |
108 | |
109 BLATFile.close() | |
110 | |
111 def createDictOfSsrParser(self, dictSsrParser): | |
112 dictSsrParser = {} | |
113 SSRFile = open(self._inputFileSSR, 'r') | |
114 | |
115 header = SSRFile.readline() | |
116 line = SSRFile.readline() | |
117 numberLine = 2 | |
118 | |
119 while line != '' and line != '\n': | |
120 thisSSRHit = SsrParser() | |
121 thisSSRHit.setAttributesFromString(line, numberLine) | |
122 | |
123 BESName = thisSSRHit.getBesName() | |
124 if not BESName in dictSsrParser: | |
125 list = [thisSSRHit] | |
126 dictSsrParser[BESName] = list | |
127 else: | |
128 list = dictSsrParser[BESName] | |
129 list.append(thisSSRHit) | |
130 dictSsrParser[BESName] = list | |
131 | |
132 line = SSRFile.readline() | |
133 numberLine = numberLine + 1 | |
134 | |
135 SSRFile.close() | |
136 return dictSsrParser | |
137 | |
138 def createListOfGFFLinesForThisBesWithSSR(self, BlatHitObject, dictSsrParser): | |
139 listGffLines = [] | |
140 | |
141 besNameToKeep = BlatHitObject.getQName() | |
142 lOfSSRHitObject = dictSsrParser[besNameToKeep] | |
143 | |
144 for SSRHitObject in lOfSSRHitObject: | |
145 posSSRStart = self.convertSSRPositionsToChromPositions(SSRHitObject.getSsrStart(), BlatHitObject.getTStart(), BlatHitObject.getTEnd(), BlatHitObject.getStrand()) | |
146 posSSREnd = self.convertSSRPositionsToChromPositions(SSRHitObject.getSsrEnd(), BlatHitObject.getTStart(), BlatHitObject.getTEnd(), BlatHitObject.getStrand()) | |
147 ssrSeq = self.getSsrSeq(SSRHitObject.getSsrMotif(), SSRHitObject.getSsrMotifNumber()) | |
148 | |
149 col1 = BlatHitObject.getTName() | |
150 col2 = 'CrossSsrAndBesAlignedByBlat' | |
151 if self._methodName != '' and self._methodName != None: | |
152 col3 = '%s:SSR' %self._methodName | |
153 else: | |
154 col3 = 'SSR' | |
155 col4 = posSSRStart | |
156 col5 = posSSREnd | |
157 col6 = '.' | |
158 col7 = BlatHitObject.getStrand() | |
159 col8 = '.' | |
160 col9 = 'ID=SSR_%s_%s;Name=SSR_%s_%s;bes_name=%s;bes_size=%s;bes_matchstart=%s;bes_matchend=%s;bes_redundancy=%s;ssr_type=%s;ssr_motif=%s;ssr_motif_number=%s;ssr_start=%s;ssr_end=%s;muscadine_seq=%s' % (besNameToKeep, SSRHitObject.getBesRedundancy(), | |
161 besNameToKeep, SSRHitObject.getBesRedundancy(), | |
162 besNameToKeep, BlatHitObject.getQSize(), | |
163 BlatHitObject.getQStart(), BlatHitObject.getQEnd(), | |
164 SSRHitObject.getBesRedundancy(), SSRHitObject.getSsrNbNucleotides(), | |
165 SSRHitObject.getSsrMotif(), SSRHitObject.getSsrMotifNumber(), | |
166 SSRHitObject.getSsrStart(), SSRHitObject.getSsrEnd(), ssrSeq) | |
167 gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9) | |
168 listGffLines.append(gffLine) | |
169 | |
170 return listGffLines | |
171 | |
172 def convertSSRPositionsToChromPositions(self, ssrPos, chromPosStart, chromPosEnd, strand): | |
173 if strand == '+': | |
174 newPos = int(chromPosStart) + int(ssrPos) - 1 | |
175 elif strand == '-': | |
176 newPos = int(chromPosEnd) - int(ssrPos) + 1 | |
177 return newPos | |
178 | |
179 def getSsrSeq(self, motif, nbMotif): | |
180 ssrSeq = motif * int(nbMotif) | |
181 return ssrSeq | |
182 | |
183 def _createGFFOutputFile(self): | |
184 GFFfile = open(self._outputFileGFF, 'w') | |
185 GFFfile.write("##gff-version 3\n") | |
186 GFFfile.close() | |
187 | |
188 def _printGFFLinesToOutputFile(self, lLinesToPrint): | |
189 GFFfile = open(self._outputFileGFF, 'a') | |
190 for line in lLinesToPrint: | |
191 GFFfile.write(line) | |
192 GFFfile.close() | |
193 | |
194 if __name__ == '__main__': | |
195 iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff() | |
196 iCrossSsrAndBesMappedByBlatToGff.setAttributesFromCmdLine() | |
197 iCrossSsrAndBesMappedByBlatToGff.run() |