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+ − 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"}
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+ − 47 TAGS_SENSE = {-1: "antisense", 0: "", 1: "collinear"}
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+ − 48 STRANDSTOSTR = {-1: "(-)", 0: "", 1: "(+)"}
+ − 49
+ − 50
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+ − 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())
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+ − 59
+ − 60
+ − 61 class GetFlanking(object):
+ − 62
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+ − 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"
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+ − 74
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+ − 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)
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+ − 84
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+ − 85 def setOutputFile(self, fileName):
+ − 86 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
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+ − 87
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+ − 88 def addUpstreamDirection(self, upstream):
+ − 89 if upstream:
+ − 90 self.directions.append(-1)
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+ − 91
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+ − 92 def addDownstreamDirection(self, downstream):
+ − 93 if downstream:
+ − 94 self.directions.append(1)
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+ − 95
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+ − 96 def setColinear(self, colinear):
+ − 97 self.colinear = colinear
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+ − 98
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+ − 99 def setAntisense(self, antisense):
+ − 100 self.antisense = antisense
+ − 101
+ − 102 def setNoOverlap(self, noOverlap):
+ − 103 self.noOverlap = noOverlap
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+ − 104
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+ − 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
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+ − 113
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+ − 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()
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+ − 155
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+ − 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
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+ − 171
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+ − 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()
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+ − 190
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+ − 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()
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+ − 199
+ − 200 if __name__ == "__main__":
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+ − 201
+ − 202 description = "Get Flanking v1.0.1: Get the flanking regions of a set of reference. [Category: Data Selection]"
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+ − 203
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+ − 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()
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+ − 220
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+ − 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()
