Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/CompareOverlappingSmallQuery.py @ 46:169d364ddd91

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Uploaded
author m-zytnicki
date Mon, 30 Sep 2013 03:19:26 -0400
parents 44d5973c188c
children 2ac71607aa60
comparison
equal deleted inserted replaced
45:e454402ba9d9 46:169d364ddd91
72 self.invert = False 72 self.invert = False
73 self.antisense = False 73 self.antisense = False
74 self.collinear = False 74 self.collinear = False
75 self.pcOverlapQuery = False 75 self.pcOverlapQuery = False
76 self.pcOverlapRef = False 76 self.pcOverlapRef = False
77 self.minOverlap = False
78 self.included = False
79 self.including = False
80 self.bins = {} 77 self.bins = {}
81 self.overlaps = {} 78 self.overlaps = {}
82 self.notOverlapping = False 79 self.notOverlapping = False
83 80
84 def setReferenceFile(self, fileName, format): 81 def setReferenceFile(self, fileName, format):
107 self.antisense = boolean 104 self.antisense = boolean
108 105
109 def setMinPercentOverlap(self, pcOverlapQuery, pcOverlapRef): 106 def setMinPercentOverlap(self, pcOverlapQuery, pcOverlapRef):
110 self.pcOverlapQuery = pcOverlapQuery 107 self.pcOverlapQuery = pcOverlapQuery
111 self.pcOverlapRef = pcOverlapRef 108 self.pcOverlapRef = pcOverlapRef
112
113 def setMinOverlap(self, minOverlap):
114 self.minOverlap = minOverlap
115
116 def setInclude(self, included, including):
117 self.included = included
118 self.including = including
119 109
120 def includeNotOverlapping(self, boolean): 110 def includeNotOverlapping(self, boolean):
121 self.notOverlapping = boolean 111 self.notOverlapping = boolean
122 112
123 def loadQuery(self): 113 def loadQuery(self):
143 return False 133 return False
144 if self.collinear and queryTranscript.getDirection() != refTranscript.getDirection(): 134 if self.collinear and queryTranscript.getDirection() != refTranscript.getDirection():
145 return False 135 return False
146 if self.antisense and queryTranscript.getDirection() == refTranscript.getDirection(): 136 if self.antisense and queryTranscript.getDirection() == refTranscript.getDirection():
147 return False 137 return False
148 if self.included and not refTranscript.include(queryTranscript):
149 return False
150 if self.including and not queryTranscript.include(refTranscript):
151 return False
152 querySize = queryTranscript.getSize() 138 querySize = queryTranscript.getSize()
153 if self.pcOverlapQuery and not queryTranscript.overlapWithExon(refTranscript, int(querySize * self.pcOverlapQuery / 100.0)): 139 if self.pcOverlapQuery and not queryTranscript.overlapWithExon(refTranscript, int(querySize * self.pcOverlapQuery / 100.0)):
154 return False 140 return False
155 refSize = refTranscript.getSize() 141 refSize = refTranscript.getSize()
156 if self.pcOverlapRef and not queryTranscript.overlapWithExon(refTranscript, int(refSize * self.pcOverlapRef / 100.0)): 142 if self.pcOverlapRef and not queryTranscript.overlapWithExon(refTranscript, int(refSize * self.pcOverlapRef / 100.0)):
157 return False
158 if self.minOverlap and not queryTranscript.overlapWithExon(refTranscript, self.minOverlap):
159 return False 143 return False
160 return True 144 return True
161 145
162 def _alterTranscript(self, transcript, type): 146 def _alterTranscript(self, transcript, type):
163 if type == REFERENCE: 147 if type == REFERENCE:
235 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]") 219 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
236 parser.add_option("-O", "--notOverlapping", dest="notOverlapping", action="store_true", default=False, help="also output not overlapping data [format: bool] [default: false]") 220 parser.add_option("-O", "--notOverlapping", dest="notOverlapping", action="store_true", default=False, help="also output not overlapping data [format: bool] [default: false]")
237 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="accept some distance between query and reference [format: int]") 221 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="accept some distance between query and reference [format: int]")
238 parser.add_option("-c", "--collinear", dest="collinear", action="store_true", default=False, help="provide collinear features [format: bool] [default: false]") 222 parser.add_option("-c", "--collinear", dest="collinear", action="store_true", default=False, help="provide collinear features [format: bool] [default: false]")
239 parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="provide antisense features [format: bool] [default: false]") 223 parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="provide antisense features [format: bool] [default: false]")
240 parser.add_option("-m", "--minOverlap", dest="minOverlap", action="store", default=False, type="int", help="min. #nt overlap [format: bool] [default: false]")
241 parser.add_option("-p", "--pcOverlapQuery", dest="pcOverlapQuery", action="store", default=False, type="int", help="min. % overlap of the query [format: bool] [default: false]") 224 parser.add_option("-p", "--pcOverlapQuery", dest="pcOverlapQuery", action="store", default=False, type="int", help="min. % overlap of the query [format: bool] [default: false]")
242 parser.add_option("-P", "--pcOverlapRef", dest="pcOverlapRef", action="store", default=False, type="int", help="min. % overlap of the reference [format: bool] [default: false]") 225 parser.add_option("-P", "--pcOverlapRef", dest="pcOverlapRef", action="store", default=False, type="int", help="min. % overlap of the reference [format: bool] [default: false]")
243 parser.add_option("-k", "--included", dest="included", action="store_true", default=False, help="provide query elements which are nested in reference elements [format: bool] [default: false]")
244 parser.add_option("-K", "--including", dest="including", action="store_true", default=False, help="provide query elements in which reference elements are nested [format: bool] [default: false]")
245 parser.add_option("-x", "--exclude", dest="exclude", action="store_true", default=False, help="invert the match [format: bool] [default: false]") 226 parser.add_option("-x", "--exclude", dest="exclude", action="store_true", default=False, help="invert the match [format: bool] [default: false]")
246 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") 227 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
247 (options, args) = parser.parse_args() 228 (options, args) = parser.parse_args()
248 229
249 cosq = CompareOverlappingSmallQuery(options.verbosity) 230 cosq = CompareOverlappingSmallQuery(options.verbosity)
253 cosq.includeNotOverlapping(options.notOverlapping) 234 cosq.includeNotOverlapping(options.notOverlapping)
254 cosq.setDistance(options.distance) 235 cosq.setDistance(options.distance)
255 cosq.setCollinear(options.collinear) 236 cosq.setCollinear(options.collinear)
256 cosq.setAntisense(options.antisense) 237 cosq.setAntisense(options.antisense)
257 cosq.setMinPercentOverlap(options.pcOverlapQuery, options.pcOverlapRef) 238 cosq.setMinPercentOverlap(options.pcOverlapQuery, options.pcOverlapRef)
258 cosq.setMinOverlap(options.minOverlap)
259 cosq.setInclude(options.included, options.including)
260 cosq.setInvert(options.exclude) 239 cosq.setInvert(options.exclude)
261 cosq.run() 240 cosq.run()