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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2012
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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 import os, struct, time, random
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32 from optparse import OptionParser
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33 from commons.core.parsing.ParserChooser import ParserChooser
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34 from commons.core.writer.Gff3Writer import Gff3Writer
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36 from SMART.Java.Python.structure.Interval import Interval
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37 from SMART.Java.Python.ncList.NCList import NCList
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38 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
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39 from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, NCListFileUnpickle
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40 from SMART.Java.Python.ncList.FileSorter import FileSorter
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41 from SMART.Java.Python.misc.Progress import Progress
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42 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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43 from SMART.Java.Python.misc import Utils
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44 try:
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45 import cPickle as pickle
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46 except:
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47 import pickle
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48
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49 REFERENCE = 0
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50 QUERY = 1
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51 TYPES = (REFERENCE, QUERY)
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52 TYPETOSTRING = {0: "reference", 1: "query"}
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53
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54 class RestrictFromCoverage(object):
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55
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56 def __init__(self, verbosity = 1):
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57 self._verbosity = verbosity
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58 self._randomNumber = random.randint(0, 100000)
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59 self._nbWritten = 0
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60 self._nbLines = dict([type, 0] for type in TYPES)
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61 self._splittedFileNames = dict([type, {}] for type in TYPES)
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62 self._nbElementsPerChromosome = dict([type, {}] for type in TYPES)
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63 self._nbElements = dict([type, 0] for type in TYPES)
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64
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65 def __del__(self):
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66 pass
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67
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68 def _close(self):
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69 self._writer.close()
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70
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71 def setInputFileName(self, fileName, format, type):
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72 chooser = ParserChooser(self._verbosity)
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73 chooser.findFormat(format)
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74 parser = chooser.getParser(fileName)
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75 sortedFileName = "%s_%d_%d_sorted.pkl" % (os.path.splitext(fileName)[0], self._randomNumber, type)
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76 if self._verbosity > 2:
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77 print "Preparing %s file..." % (TYPETOSTRING[type])
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78 startTime = time.time()
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79 fs = FileSorter(parser, self._verbosity-1)
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80 fs.perChromosome(True)
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81 fs.setOutputFileName(sortedFileName)
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82 fs.sort()
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83 self._nbLines[type] = fs.getNbElements()
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84 self._splittedFileNames[type] = fs.getOutputFileNames()
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85 self._nbElementsPerChromosome[type] = fs.getNbElementsPerChromosome()
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86 self._nbElements[type] = fs.getNbElements()
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87 endTime = time.time()
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88 if self._verbosity > 2:
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89 print " ...done (%ds)" % (endTime - startTime)
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90
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91 def setOutputFileName(self, outputFileName):
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92 self._writer = Gff3Writer(outputFileName)
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93
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94 def setPercent(self, minPercent, maxPercent):
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95 self._minPercent = minPercent
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96 self._maxPercent = maxPercent
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97
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98 def setNbNucleotides(self, minNb, maxNb):
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99 self._minNucleotides = minNb
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100 self._maxNucleotides = maxNb
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101
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102 def setOverlap(self, minOverlap, maxOverlap):
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103 self._minOverlap = minOverlap
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104 self._maxOverlap = maxOverlap
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105
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106 def setStrands(self, boolean):
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107 self._twoStrands = boolean
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108
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109 def _compareChromosome(self, chromosome):
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110 firstOverlap = 0
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111 parser1 = NCListFileUnpickle(self._splittedFileNames[QUERY][chromosome], self._verbosity)
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112 parser2 = NCListFileUnpickle(self._splittedFileNames[REFERENCE][chromosome], self._verbosity)
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113 progress = Progress(self._nbElementsPerChromosome[QUERY][chromosome], "Analyzing %s" % (chromosome), self._verbosity)
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114 for transcript1 in parser1.getIterator():
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115 firstOverlap = self._compareList(transcript1, parser2)
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116 parser2.setInitAddress(firstOverlap)
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117 progress.inc()
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118 progress.done()
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119
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120 def _compareList(self, transcript1, parser2):
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121 values = []
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122 for exon in transcript1.getExons():
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123 values.append([0.0] * exon.getSize())
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124 firstOverlap = None
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125 for transcript2 in parser2.getIterator():
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126 address = parser2.getCurrentTranscriptAddress()
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127 nbElements = float(transcript2.getTagValue("nbElements")) if "nbElements" in transcript2.getTagNames() else 1.0
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128 nbOccurrences = float(transcript2.getTagValue("nbOccurrences")) if "nbOccurrences" in transcript2.getTagNames() else 1.0
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129 nbElements /= nbOccurrences
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130 if transcript2.getStart() > transcript1.getEnd():
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131 if firstOverlap == None:
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132 firstOverlap = address
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133 if self._checkValues(values):
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134 self._printTranscript(transcript1)
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135 return firstOverlap
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136 elif transcript1.overlapWith(transcript2):
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137 if firstOverlap == None:
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138 firstOverlap = address
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139 values = self._compareTranscript(transcript1, transcript2, values, nbElements)
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140 if self._checkValues(values):
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141 self._printTranscript(transcript1)
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142 return firstOverlap
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143
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144 def _compareTranscript(self, transcript1, transcript2, values, nbElements):
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145 if not transcript1.overlapWith(transcript2) or ((self._twoStrands) and transcript1.getDirection() != transcript2.getDirection()):
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146 return values
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147 for id1, exon1 in enumerate(transcript1.getExons()):
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148 for exon2 in transcript2.getExons():
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149 values[id1] = map(sum, zip(values[id1], self._compareExon(exon1, exon2, nbElements)))
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150 return values
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151
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152 def _compareExon(self, exon1, exon2, nbElements):
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153 array = [0.0] * exon1.getSize()
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154 if not exon1.overlapWith(exon2) or ((self._twoStrands) and exon1.getDirection() != exon2.getDirection()):
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155 return array
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156 for pos in range(max(exon1.getStart(), exon2.getStart()) - exon1.getStart(), min(exon1.getEnd(), exon2.getEnd()) - exon1.getStart()+1):
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157 array[pos] += nbElements
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158 return array
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159
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160 def _filter(self, value):
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161 if self._minOverlap and self._maxOverlap:
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162 return self._minOverlap <= value <= self._maxOverlap
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163 if self._minOverlap:
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164 return self._minOverlap <= value
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165 if self._maxOverlap:
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166 return value <= self._maxOverlap
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167 return True
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168
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169 def _checkValues(self, values):
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170 nbValues = sum(map(len, values))
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171 nbPosValues = sum(map(len, [filter(self._filter, valuePart) for valuePart in values]))
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172 ratio = float(nbPosValues) / nbValues * 100
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173 if self._minNucleotides and nbPosValues < self._minNucleotides:
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174 return False
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175 if self._maxNucleotides and nbPosValues > self._maxNucleotides:
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176 return False
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177 if self._minPercent and ratio < self._minPercent:
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178 return False
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179 if self._maxPercent and ratio > self._maxPercent:
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180 return False
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181 return True
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182
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183 def _printTranscript(self, transcript):
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184 self._writer.addTranscript(transcript)
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185 self._nbWritten += 1
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186
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187 def run(self):
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188 for chromosome in sorted(self._splittedFileNames[QUERY].keys()):
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189 self._compareChromosome(chromosome)
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190 self._close()
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191 if self._verbosity > 0:
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192 print "# queries: %d" % (self._nbElements[QUERY])
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193 print "# refs: %d" % (self._nbElements[REFERENCE])
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194 print "# written: %d (%d%%)" % (self._nbWritten, 0 if self._nbElements[QUERY] == 0 else round(float(self._nbWritten) / self._nbElements[QUERY] * 100))
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195
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196
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197 if __name__ == "__main__":
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198 description = "Restrict From Coverage v1.0.0: Select the elements from the first set which have a given coverage. [Category: Data Comparison]"
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199
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200 parser = OptionParser(description = description)
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201 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
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202 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]")
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203 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
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204 parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of file 2 [compulsory] [format: transcript file format]")
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205 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
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206 parser.add_option("-n", "--minNucleotides", dest="minNucleotides", action="store", default=None, type="int", help="minimum number of nucleotides overlapping to declare an overlap [format: int]")
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207 parser.add_option("-N", "--maxNucleotides", dest="maxNucleotides", action="store", default=None, type="int", help="maximum number of nucleotides overlapping to declare an overlap [format: int]")
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208 parser.add_option("-p", "--minPercent", dest="minPercent", action="store", default=None, type="int", help="minimum percentage of nucleotides overlapping to declare an overlap [format: int]")
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209 parser.add_option("-P", "--maxPercent", dest="maxPercent", action="store", default=None, type="int", help="maximum percentage of nucleotides overlapping to declare an overlap [format: int]")
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210 parser.add_option("-e", "--minOverlap", dest="minOverlap", action="store", default=None, type="int", help="minimum number of elements from 2nd file to declare an overlap [format: int]")
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211 parser.add_option("-E", "--maxOverlap", dest="maxOverlap", action="store", default=None, type="int", help="maximum number of elements from 2nd file to declare an overlap [format: int]")
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212 parser.add_option("-s", "--strands", dest="strands", action="store_true", default=False, help="consider the two strands separately [format: bool] [default: false]")
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213 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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214 (options, args) = parser.parse_args()
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215
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216 rfc = RestrictFromCoverage(options.verbosity)
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217 rfc.setInputFileName(options.inputFileName1, options.format1, QUERY)
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218 rfc.setInputFileName(options.inputFileName2, options.format2, REFERENCE)
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219 rfc.setOutputFileName(options.output)
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220 rfc.setNbNucleotides(options.minNucleotides, options.maxNucleotides)
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221 rfc.setPercent(options.minPercent, options.maxPercent)
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222 rfc.setOverlap(options.minOverlap, options.maxOverlap)
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223 rfc.setStrands(options.strands)
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224 rfc.run()
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