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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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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
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32 import os, struct, time
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33 from optparse import OptionParser
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34 from commons.core.parsing.ParserChooser import ParserChooser
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36 from SMART.Java.Python.ncList.NCList import NCList
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37 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
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38 from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, NCListFileUnpickle
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39 from SMART.Java.Python.ncList.FileSorter import FileSorter
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40 from SMART.Java.Python.misc.Progress import Progress
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41 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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42 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
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43 from SMART.Java.Python.ncList.FindOverlapsWithOneInterval import FindOverlapsWithOneInterval
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44
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45 REFERENCE = 0
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46 QUERY = 1
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47 TYPETOSTRING = {0: "reference", 1: "query"}
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48
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49 class FindOverlapsWithSeveralIntervals(object):
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50
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51 def __init__(self, verbosity = 1):
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52 self._parsers = {}
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53 self._outputFileName = "outputOverlaps.gff3"
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54 self._iWriter = None
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55 self._nbLines = {REFERENCE: 0, QUERY: 0}
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56 self._verbosity = verbosity
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57 self._ncLists = {}
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58 self._sortedRefFileNames = None
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59 self._transQueryFileName = None
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60 self._cursors = {}
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61 self._iFowoi = FindOverlapsWithOneInterval(self._verbosity)
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62
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63 def __del__(self):
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64 self.close()
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65 for fileName in (self._sortedRefFileNames, self._transQueryFileName):
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66 if os.path.exists(fileName):
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67 os.remove(fileName)
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68
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69 def close(self):
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70 self._iFowoi.close()
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71
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72 def setRefFileName(self, fileName, format):
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73 self.setFileName(fileName, format, REFERENCE)
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74 self._sortedRefFileNames = "%s_ref_sorted.pkl" % (os.path.splitext(fileName)[0])
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75
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76 def setQueryFileName(self, fileName, format):
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77 self.setFileName(fileName, format, QUERY)
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78 self._transQueryFileName = "%s_query_trans.pkl" % (os.path.splitext(fileName)[0])
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79
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80 def setFileName(self, fileName, format, type):
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81 chooser = ParserChooser(self._verbosity)
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82 chooser.findFormat(format)
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83 self._parsers[type] = chooser.getParser(fileName)
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84
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85 def setOutputFileName(self, outputFileName):
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86 self._iFowoi.setOutputFileName(outputFileName)
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87
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88 def _sortRefFile(self):
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89 fs = FileSorter(self._parsers[REFERENCE], self._verbosity-4)
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90 fs.perChromosome(True)
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91 fs.setOutputFileName(self._sortedRefFileNames)
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92 fs.sort()
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93 self._nbLines[REFERENCE] = fs.getNbElements()
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94 self._nbRefLinesPerChromosome = fs.getNbElementsPerChromosome()
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95 self._splittedFileNames = fs.getOutputFileNames()
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96
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97 def _translateQueryFile(self):
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98 pickler = NCListFilePickle(self._transQueryFileName, self._verbosity)
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99 progress = UnlimitedProgress(1000, "Translating query data", self._verbosity-4)
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100 cpt = 0
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101 for queryTranscript in self._parsers[QUERY].getIterator():
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102 pickler.addTranscript(queryTranscript)
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103 progress.inc()
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104 cpt += 1
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105 progress.done()
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106 self._nbLines[QUERY] = cpt
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107 self._parsers[QUERY] = NCListFileUnpickle(self._transQueryFileName, self._verbosity)
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108
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109 def prepareIntermediateFiles(self):
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110 self._sortRefFile()
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111 self._translateQueryFile()
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112
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113 def createNCLists(self):
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114 self._ncLists = {}
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115 self._indices = {}
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116 self._cursors = {}
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117 for chromosome, fileName in self._splittedFileNames.iteritems():
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118 if self._verbosity > 3:
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119 print " chromosome %s" % (chromosome)
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120 ncList = NCList(self._verbosity)
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121 ncList.createIndex(True)
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122 ncList.setChromosome(chromosome)
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123 ncList.setFileName(fileName)
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124 ncList.setNbElements(self._nbRefLinesPerChromosome[chromosome])
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125 ncList.buildLists()
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126 self._ncLists[chromosome] = ncList
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127 cursor = NCListCursor(None, ncList, 0, self._verbosity)
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128 self._cursors[chromosome] = cursor
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129 self._indices[chromosome] = ncList.getIndex()
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130 endTime = time.time()
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131
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132 def compare(self):
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133 progress = Progress(self._nbLines[QUERY], "Comparing data", self._verbosity-3)
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134 startTime = time.time()
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135 for cpt, queryTranscript in enumerate(self._parsers[QUERY].getIterator()):
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136 chromosome = queryTranscript.getChromosome()
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137 if chromosome not in self._ncLists:
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138 continue
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139 self._iFowoi.setNCList(self._ncLists[chromosome], self._indices[chromosome])
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140 self._iFowoi.setTranscript(queryTranscript)
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141 self._iFowoi.compare()
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142 self._iFowoi.dumpWriter()
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143 progress.inc()
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144 progress.done()
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145 endTime = time.time()
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146 self._timeSpent = endTime - startTime
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147
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148 def run(self):
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149 startTime = time.time()
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150 if self._verbosity > 2:
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151 print "Creating NC-list..."
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152 self.prepareIntermediateFiles()
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153 self.createNCLists()
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154 endTime = time.time()
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155 if self._verbosity > 2:
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156 print " ...done (%.2gs)" % (endTime - startTime)
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157 self.compare()
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158 self.close()
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159 if self._verbosity > 0:
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160 print "# queries: %d" % (self._nbLines[QUERY])
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161 print "# refs: %d" % (self._nbLines[REFERENCE])
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162 print "# written: %d (%d overlaps)" % (self._iFowoi._nbWritten, self._iFowoi._nbOverlaps)
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163 print "time: %.2gs" % (self._timeSpent)
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164
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165
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166 if __name__ == "__main__":
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167 description = "FindOverlaps With Several Intervals v1.0.0: Finds overlaps with several query intervals. [Category: Data comparison]"
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168
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169 parser = OptionParser(description = description)
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170 parser.add_option("-i", "--query", dest="inputQueryFileName", action="store", type="string", help="Query input file [compulsory] [format: file in transcript format given by -f]")
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171 parser.add_option("-f", "--queryFormat", dest="queryFormat", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
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172 parser.add_option("-j", "--ref", dest="inputRefFileName", action="store", type="string", help="Reference input file [compulsory] [format: file in transcript format given by -g]")
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173 parser.add_option("-g", "--refFormat", dest="refFormat", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]")
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174 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="Output file [compulsory] [format: output file in GFF3 format]")
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175 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="Trace level [format: int] [default: 1]")
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176 (options, args) = parser.parse_args()
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177
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178 iFWSI = FindOverlapsWithSeveralIntervals(options.verbosity)
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179 iFWSI.setRefFileName(options.inputRefFileName, options.refFormat)
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180 iFWSI.setQueryFileName(options.inputQueryFileName, options.queryFormat)
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181 iFWSI.setOutputFileName(options.outputFileName)
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182 iFWSI.run()
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