|
6
|
1 #! /usr/bin/env python
|
|
|
2 #
|
|
|
3 # Copyright INRA-URGI 2009-2011
|
|
|
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 from optparse import OptionParser
|
|
|
32 from commons.core.parsing.ParserChooser import ParserChooser
|
|
|
33 from commons.core.writer.TranscriptWriter import TranscriptWriter
|
|
|
34 from SMART.Java.Python.structure.Transcript import Transcript
|
|
|
35 from SMART.Java.Python.structure.Interval import Interval
|
|
|
36 from SMART.Java.Python.misc.Progress import Progress
|
|
|
37
|
|
|
38 QUERY = 0
|
|
|
39 REFERENCE = 1
|
|
|
40 INPUTS = (QUERY, REFERENCE)
|
|
|
41 STRANDS = (-1, 1)
|
|
|
42 TAG_DISTANCE = "distance_"
|
|
|
43 TAG_SENSE = "_sense"
|
|
|
44 TAG_REGION = "_region"
|
|
|
45 TAGS_REGION = {-1: "_upstream", 0: "", 1: "_downstream"}
|
|
|
46 TAGS_RREGION = {-1: "upstream", 0: "overlapping", 1: "downstream"}
|
|
18
|
47 TAGS_SENSE = {-1: "antisense", 0: "", 1: "collinear"}
|
|
6
|
48 STRANDSTOSTR = {-1: "(-)", 0: "", 1: "(+)"}
|
|
|
49
|
|
|
50
|
|
18
|
51 def getOrderKey(transcript, direction, input):
|
|
|
52 if direction == 1:
|
|
|
53 if input == QUERY:
|
|
|
54 return (transcript.getEnd(), -transcript.getStart())
|
|
|
55 return (transcript.getStart(), -transcript.getEnd())
|
|
|
56 if input == QUERY:
|
|
|
57 return (-transcript.getStart(), transcript.getEnd())
|
|
|
58 return (-transcript.getEnd(), transcript.getStart())
|
|
6
|
59
|
|
|
60
|
|
|
61 class GetFlanking(object):
|
|
|
62
|
|
18
|
63 def __init__(self, verbosity):
|
|
|
64 self.verbosity = verbosity
|
|
|
65 self.transcripts = dict([id, {}] for id in INPUTS)
|
|
|
66 self.directions = []
|
|
|
67 self.noOverlap = False
|
|
|
68 self.colinear = False
|
|
|
69 self.antisense = False
|
|
|
70 self.distance = None
|
|
|
71 self.minDistance = None
|
|
|
72 self.maxDistance = None
|
|
|
73 self.tagName = "flanking"
|
|
6
|
74
|
|
18
|
75 def setInputFile(self, fileName, format, id):
|
|
|
76 chooser = ParserChooser(self.verbosity)
|
|
|
77 chooser.findFormat(format)
|
|
|
78 parser = chooser.getParser(fileName)
|
|
|
79 for transcript in parser.getIterator():
|
|
|
80 chromosome = transcript.getChromosome()
|
|
|
81 if chromosome not in self.transcripts[id]:
|
|
|
82 self.transcripts[id][chromosome] = []
|
|
|
83 self.transcripts[id][chromosome].append(transcript)
|
|
6
|
84
|
|
18
|
85 def setOutputFile(self, fileName):
|
|
|
86 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
|
|
6
|
87
|
|
18
|
88 def addUpstreamDirection(self, upstream):
|
|
|
89 if upstream:
|
|
|
90 self.directions.append(-1)
|
|
6
|
91
|
|
18
|
92 def addDownstreamDirection(self, downstream):
|
|
|
93 if downstream:
|
|
|
94 self.directions.append(1)
|
|
6
|
95
|
|
18
|
96 def setColinear(self, colinear):
|
|
|
97 self.colinear = colinear
|
|
6
|
98
|
|
18
|
99 def setAntisense(self, antisense):
|
|
|
100 self.antisense = antisense
|
|
|
101
|
|
|
102 def setNoOverlap(self, noOverlap):
|
|
|
103 self.noOverlap = noOverlap
|
|
6
|
104
|
|
18
|
105 def setMinDistance(self, distance):
|
|
|
106 self.minDistance = distance
|
|
|
107
|
|
|
108 def setMaxDistance(self, distance):
|
|
|
109 self.maxDistance = distance
|
|
|
110
|
|
|
111 def setNewTagName(self, tagName):
|
|
|
112 self.tagName = tagName
|
|
6
|
113
|
|
18
|
114 def match(self, transcriptQuery, transcriptRef, direction):
|
|
|
115 #print "comparing", transcriptQuery, "with", transcriptRef, "on direction", direction
|
|
|
116 if direction == 1 and transcriptRef.getEnd() < transcriptQuery.getStart():
|
|
|
117 return False
|
|
|
118 if direction == -1 and transcriptQuery.getEnd() < transcriptRef.getStart():
|
|
|
119 return False
|
|
|
120 if self.noOverlap and transcriptRef.overlapWith(transcriptQuery):
|
|
|
121 return False
|
|
|
122 if self.colinear and transcriptRef.getDirection() != transcriptQuery.getDirection():
|
|
|
123 return False
|
|
|
124 if self.antisense and transcriptRef.getDirection() == transcriptQuery.getDirection():
|
|
|
125 return False
|
|
|
126 if self.minDistance != None or self.maxDistance != None:
|
|
|
127 distance = transcriptRef.getDistance(transcriptQuery)
|
|
|
128 if self.minDistance != None and distance < self.minDistance:
|
|
|
129 return False
|
|
|
130 if self.maxDistance != None and distance > self.maxDistance:
|
|
|
131 return False
|
|
|
132 return True
|
|
|
133
|
|
|
134 def getFlanking(self, chromosome, direction):
|
|
|
135 if chromosome not in self.transcripts[REFERENCE]:
|
|
|
136 return
|
|
|
137 sortedTranscripts = dict([id, {}] for id in INPUTS)
|
|
|
138 for id in INPUTS:
|
|
|
139 sortedTranscripts[id] = sorted(self.transcripts[id][chromosome], key = lambda t: getOrderKey(t, direction, id))
|
|
|
140 refIndex = 0
|
|
|
141 progress = Progress(len(sortedTranscripts[QUERY]), "Reading chr %s %s" % (chromosome, STRANDSTOSTR[direction]), self.verbosity)
|
|
|
142 for query in sortedTranscripts[QUERY]:
|
|
|
143 #print "Q: ", query
|
|
|
144 #print "R1: ", sortedTranscripts[REFERENCE][refIndex]
|
|
|
145 while not self.match(query, sortedTranscripts[REFERENCE][refIndex], direction):
|
|
|
146 refIndex += 1
|
|
|
147 if refIndex == len(sortedTranscripts[REFERENCE]):
|
|
|
148 progress.done()
|
|
|
149 #print "done"
|
|
|
150 return
|
|
|
151 #print "R2: ", sortedTranscripts[REFERENCE][refIndex]
|
|
|
152 self.flankings[query][direction] = sortedTranscripts[REFERENCE][refIndex]
|
|
|
153 progress.inc()
|
|
|
154 progress.done()
|
|
6
|
155
|
|
18
|
156 def setTags(self, query, reference, direction):
|
|
|
157 refName = reference.getTagValue("ID")
|
|
|
158 if refName == None:
|
|
|
159 refName = reference.getName()
|
|
|
160 if refName == None:
|
|
|
161 refName = reference.__str__()
|
|
|
162 query.setTagValue("%s%s" % (self.tagName, TAGS_REGION[direction*query.getDirection()]), refName)
|
|
|
163 query.setTagValue("%s_%s%s" % (TAG_DISTANCE, self.tagName, TAGS_REGION[direction*query.getDirection()]), query.getDistance(reference))
|
|
|
164 query.setTagValue("%s_%s" % (TAG_SENSE, self.tagName), TAGS_SENSE[query.getDirection() * reference.getDirection()])
|
|
|
165 if direction == 0:
|
|
|
166 query.setTagValue("%s_%s" % (TAG_REGION, self.tagName), TAGS_RREGION[cmp(query.getRelativeDistance(reference), 0)])
|
|
|
167 for tag in reference.getTagNames():
|
|
|
168 if tag not in ("quality", "feature"):
|
|
|
169 query.setTagValue("%s%s_%s" % (self.tagName, TAGS_REGION[direction*query.getDirection()], tag), reference.getTagValue(tag))
|
|
|
170 return query
|
|
6
|
171
|
|
18
|
172 def write(self):
|
|
|
173 progress = Progress(len(self.flankings.keys()), "Printing data", self.verbosity)
|
|
|
174 for transcriptQuery in self.flankings.keys():
|
|
|
175 if not self.flankings[transcriptQuery]:
|
|
|
176 self.writer.addTranscript(transcriptQuery)
|
|
|
177 elif self.directions:
|
|
|
178 for direction in self.directions:
|
|
|
179 #relativeDirection = direction if transcriptQuery.getDirection() == 1 else - direction
|
|
|
180 relativeDirection = direction * transcriptQuery.getDirection()
|
|
|
181 if relativeDirection in self.flankings[transcriptQuery]:
|
|
|
182 transcriptRef = self.flankings[transcriptQuery][relativeDirection]
|
|
|
183 transcriptQuery = self.setTags(transcriptQuery, transcriptRef, relativeDirection)
|
|
|
184 self.writer.addTranscript(transcriptQuery)
|
|
|
185 else:
|
|
|
186 transcriptRef = sorted(self.flankings[transcriptQuery].values(), key = lambda transcriptRef: transcriptQuery.getDistance(transcriptRef))[0]
|
|
|
187 self.writer.addTranscript(self.setTags(transcriptQuery, transcriptRef, 0))
|
|
|
188 progress.inc()
|
|
|
189 progress.done()
|
|
6
|
190
|
|
18
|
191 def run(self):
|
|
|
192 for chromosome in sorted(self.transcripts[QUERY].keys()):
|
|
|
193 self.flankings = dict([query, {}] for query in self.transcripts[QUERY][chromosome])
|
|
|
194 for direction in STRANDS:
|
|
|
195 #print "comparison", chromosome, direction
|
|
|
196 self.getFlanking(chromosome, direction)
|
|
|
197 self.write()
|
|
|
198 self.writer.close()
|
|
6
|
199
|
|
|
200 if __name__ == "__main__":
|
|
18
|
201
|
|
|
202 description = "Get Flanking v1.0.1: Get the flanking regions of a set of reference. [Category: Data Selection]"
|
|
6
|
203
|
|
18
|
204 parser = OptionParser(description = description)
|
|
|
205 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
|
|
|
206 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
|
|
|
207 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
|
|
|
208 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
|
|
|
209 parser.add_option("-5", "--upstream", dest="upstream", action="store_true", default=False, help="output upstream elements [format: boolean] [default: False]")
|
|
|
210 parser.add_option("-3", "--downstream", dest="downstream", action="store_true", default=False, help="output downstream elements [format: boolean] [default: False]")
|
|
|
211 parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="find first colinear element [format: boolean] [default: False]")
|
|
|
212 parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="find first anti-sense element [format: boolean] [default: False]")
|
|
|
213 parser.add_option("-e", "--noOverlap", dest="noOverlap", action="store_true", default=False, help="do not consider elements which are overlapping reference elements [format: boolean] [default: False]")
|
|
|
214 parser.add_option("-d", "--minDistance", dest="minDistance", action="store", default=None, type="int", help="minimum distance between 2 elements [format: int]")
|
|
|
215 parser.add_option("-D", "--maxDistance", dest="maxDistance", action="store", default=None, type="int", help="maximum distance between 2 elements [format: int]")
|
|
|
216 parser.add_option("-t", "--tag", dest="tagName", action="store", default="flanking", type="string", help="name of the new tag [format: string] [default: flanking]")
|
|
|
217 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
|
|
|
218 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
|
|
|
219 (options, args) = parser.parse_args()
|
|
6
|
220
|
|
18
|
221 gf = GetFlanking(options.verbosity)
|
|
|
222 gf.setInputFile(options.inputFileName1, options.format1, QUERY)
|
|
|
223 gf.setInputFile(options.inputFileName2, options.format2, REFERENCE)
|
|
|
224 gf.setOutputFile(options.outputFileName)
|
|
|
225 gf.addUpstreamDirection(options.upstream)
|
|
|
226 gf.addDownstreamDirection(options.downstream)
|
|
|
227 gf.setColinear(options.colinear)
|
|
|
228 gf.setAntisense(options.antisense)
|
|
|
229 gf.setNoOverlap(options.noOverlap)
|
|
|
230 gf.setMinDistance(options.minDistance)
|
|
|
231 gf.setMaxDistance(options.maxDistance)
|
|
|
232 gf.setNewTagName(options.tagName)
|
|
|
233 gf.run()
|
