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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2011
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 from optparse import OptionParser
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32 from commons.core.parsing.ParserChooser import ParserChooser
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33 from commons.core.writer.TranscriptWriter import TranscriptWriter
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34 from SMART.Java.Python.structure.Transcript import Transcript
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35 from SMART.Java.Python.structure.Interval import Interval
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36 from SMART.Java.Python.misc.Progress import Progress
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37
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38 QUERY = 0
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39 REFERENCE = 1
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40 INPUTS = (QUERY, REFERENCE)
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41 STRANDS = (-1, 1)
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42 TAG_DISTANCE = "distance_"
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43 TAG_SENSE = "_sense"
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44 TAG_REGION = "_region"
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45 TAGS_REGION = {-1: "_upstream", 0: "", 1: "_downstream"}
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46 TAGS_RREGION = {-1: "upstream", 0: "overlapping", 1: "downstream"}
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46
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47 TAGS_SENSE = {-1: "antisense", 0: "", 1: "colinear"}
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36
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48 STRANDSTOSTR = {-1: "(-)", 0: "", 1: "(+)"}
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49
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50
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46
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51 def getOrderKey(transcript, direction):
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52 if direction == 1:
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53 return transcript.getEnd()
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54 return - transcript.getStart()
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55
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56 def isInGoodRegion(transcriptRef, transcriptQuery, direction):
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57 if direction == 1:
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58 return transcriptQuery.getEnd() > transcriptRef.getEnd()
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59 return transcriptQuery.getStart() < transcriptRef.getStart()
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36
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60
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61
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62 class GetFlanking(object):
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63
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64 def __init__(self, verbosity):
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65 self.verbosity = verbosity
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66 self.transcripts = dict([id, {}] for id in INPUTS)
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67 self.directions = []
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68 self.noOverlap = False
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69 self.colinear = False
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70 self.antisense = False
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71 self.distance = None
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72 self.minDistance = None
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73 self.maxDistance = None
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74 self.tagName = "flanking"
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75
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76 def setInputFile(self, fileName, format, id):
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77 chooser = ParserChooser(self.verbosity)
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78 chooser.findFormat(format)
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79 parser = chooser.getParser(fileName)
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80 for transcript in parser.getIterator():
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81 chromosome = transcript.getChromosome()
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82 if chromosome not in self.transcripts[id]:
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83 self.transcripts[id][chromosome] = []
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84 self.transcripts[id][chromosome].append(transcript)
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85
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86 def setOutputFile(self, fileName):
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87 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
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88
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89 def addUpstreamDirection(self, upstream):
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90 if upstream:
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91 self.directions.append(-1)
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92
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93 def addDownstreamDirection(self, downstream):
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94 if downstream:
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95 self.directions.append(1)
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96
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97 def setColinear(self, colinear):
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98 self.colinear = colinear
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99
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100 def setAntisense(self, antisense):
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101 self.antisense = antisense
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102
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103 def setNoOverlap(self, noOverlap):
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104 self.noOverlap = noOverlap
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105
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106 def setMinDistance(self, distance):
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107 self.minDistance = distance
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108
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109 def setMaxDistance(self, distance):
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110 self.maxDistance = distance
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111
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112 def setNewTagName(self, tagName):
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113 self.tagName = tagName
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114
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115 def match(self, transcriptRef, transcriptQuery, direction):
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116 if self.noOverlap and transcriptRef.overlapWith(transcriptQuery):
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117 return False
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118 if self.colinear and transcriptRef.getDirection() != transcriptQuery.getDirection():
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119 return False
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120 if self.antisense and transcriptRef.getDirection() == transcriptQuery.getDirection():
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121 return False
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122 if self.minDistance != None or self.maxDistance != None:
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123 distance = transcriptRef.getDistance(transcriptQuery)
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124 if self.minDistance != None and distance < self.minDistance:
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125 return False
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126 if self.maxDistance != None and distance > self.maxDistance:
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127 return False
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128 return True
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129
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130 def getFlanking(self, direction):
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131 for chromosome in sorted(self.transcripts[REFERENCE].keys()):
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132 if chromosome not in self.transcripts[QUERY]:
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133 continue
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134 sortedTranscripts = dict([id, {}] for id in INPUTS)
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135 for id in INPUTS:
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136 sortedTranscripts[id] = sorted(self.transcripts[id][chromosome], key = lambda t: getOrderKey(t, direction))
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137 refIndex = 0
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138 currentRefs = []
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139 outputs = set()
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140 progress = Progress(len(sortedTranscripts[QUERY]), "Reading chr %s %s" % (chromosome, STRANDSTOSTR[direction]), self.verbosity)
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141 for query in sortedTranscripts[QUERY]:
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142 while refIndex < len(sortedTranscripts[REFERENCE]) and isInGoodRegion(sortedTranscripts[REFERENCE][refIndex], query, direction):
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143 currentRefs.append(sortedTranscripts[REFERENCE][refIndex])
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144 refIndex += 1
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145 nextCurrentRefs = []
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146 for currentRef in currentRefs:
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147 if self.match(currentRef, query, direction):
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148 if currentRef not in self.flankings:
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149 self.flankings[currentRef] = {}
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150 self.flankings[currentRef][direction * currentRef.getDirection()] = query
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151 else:
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152 nextCurrentRefs.append(currentRef)
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153 currentRefs = nextCurrentRefs
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154 progress.inc()
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155 progress.done()
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156
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157 def setTags(self, query, reference, direction):
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158 refName = reference.getTagValue("ID")
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159 if refName == None:
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160 refName = reference.getName()
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161 if refName == None:
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162 refName = reference.__str__()
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163 query.setTagValue("%s%s" % (self.tagName, TAGS_REGION[direction]), refName)
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164 query.setTagValue("%s_%s%s" % (TAG_DISTANCE, self.tagName, TAGS_REGION[direction]), query.getDistance(reference))
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165 if direction == 0:
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166 query.setTagValue("%s_%s" % (TAG_SENSE, self.tagName), TAGS_SENSE[query.getDirection() * reference.getDirection()])
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167 query.setTagValue("%s_%s" % (TAG_REGION, self.tagName), TAGS_RREGION[cmp(query.getRelativeDistance(reference), 0)])
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168 for tag in reference.getTagNames():
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169 if tag not in ("quality", "feature"):
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170 query.setTagValue("%s%s_%s" % (self.tagName, TAGS_REGION[direction], tag), reference.getTagValue(tag))
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171 return query
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172
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173 def write(self):
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174 outputs = set()
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175 progress = Progress(len(self.flankings.keys()), "Printing data", self.verbosity)
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176 for transcriptRef in self.flankings.keys():
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177 if self.directions:
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178 for direction in self.directions:
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179 if direction in self.flankings[transcriptRef]:
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180 query = self.flankings[transcriptRef][direction]
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181 outputs.add(self.setTags(query, transcriptRef, direction))
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182 else:
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183 if self.flankings[transcriptRef]:
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184 query = sorted(self.flankings[transcriptRef].values(), key = lambda query: query.getDistance(transcriptRef))[0]
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185 outputs.add(self.setTags(query, transcriptRef, 0))
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186 progress.inc()
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187 for transcript in sorted(list(outputs), key = lambda flanking: (flanking.getChromosome(), flanking.getStart(), flanking.getEnd())):
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188 self.writer.addTranscript(transcript)
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189 self.writer.close()
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190 progress.done()
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191
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192 def run(self):
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193 self.flankings = {}
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194 for direction in STRANDS:
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195 self.getFlanking(direction)
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196 self.write()
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197
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198 if __name__ == "__main__":
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199
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200 description = "Get Flanking v1.0.1: Get the flanking regions of a set of reference. [Category: Data Selection]"
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201
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202 parser = OptionParser(description = description)
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203 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
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204 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
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205 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
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206 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
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207 parser.add_option("-5", "--upstream", dest="upstream", action="store_true", default=False, help="output upstream elements [format: boolean] [default: False]")
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208 parser.add_option("-3", "--downstream", dest="downstream", action="store_true", default=False, help="output downstream elements [format: boolean] [default: False]")
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209 parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="find first colinear element [format: boolean] [default: False]")
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210 parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="find first anti-sense element [format: boolean] [default: False]")
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211 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]")
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212 parser.add_option("-d", "--minDistance", dest="minDistance", action="store", default=None, type="int", help="minimum distance between 2 elements [format: int]")
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213 parser.add_option("-D", "--maxDistance", dest="maxDistance", action="store", default=None, type="int", help="maximum distance between 2 elements [format: int]")
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214 parser.add_option("-t", "--tag", dest="tagName", action="store", default="flanking", type="string", help="name of the new tag [format: string] [default: flanking]")
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215 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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216 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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217 (options, args) = parser.parse_args()
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218
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219 gf = GetFlanking(options.verbosity)
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220 gf.setInputFile(options.inputFileName1, options.format1, QUERY)
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221 gf.setInputFile(options.inputFileName2, options.format2, REFERENCE)
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222 gf.setOutputFile(options.outputFileName)
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223 gf.addUpstreamDirection(options.upstream)
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224 gf.addDownstreamDirection(options.downstream)
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225 gf.setColinear(options.colinear)
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226 gf.setAntisense(options.antisense)
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227 gf.setNoOverlap(options.noOverlap)
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228 gf.setMinDistance(options.minDistance)
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229 gf.setMaxDistance(options.maxDistance)
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230 gf.setNewTagName(options.tagName)
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231 gf.run()
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