Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Python/ncList/FindOverlapsWithOneInterval.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 struct |
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33 import math |
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34 import os |
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35 from optparse import OptionParser |
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36 from commons.core.writer.Gff3Writer import Gff3Writer |
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37 from SMART.Java.Python.ncList.NCList import NCList |
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38 from SMART.Java.Python.ncList.FileSorter import FileSorter |
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39 from commons.core.parsing.ParserChooser import ParserChooser |
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40 from SMART.Java.Python.ncList.NCListCursor import NCListCursor |
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41 from SMART.Java.Python.structure.Transcript import Transcript |
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42 |
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43 LONGSIZE = struct.calcsize('l') |
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44 |
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45 class FindOverlapsWithOneInterval(object): |
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46 |
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47 def __init__(self, verbosity): |
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48 self._sortedFileName = None |
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49 self._verbosity = verbosity |
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50 self._overlappingNames = [] |
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51 self._nbOverlaps = 0 |
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52 self._nbWritten = 0 |
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53 |
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54 def __del__(self): |
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55 if self._sortedFileName and os.path.exists(self._sortedFileName): |
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56 os.remove(self._sortedFileName) |
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57 |
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58 def close(self): |
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59 self._iWriter.close() |
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60 |
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61 def setOutputFileName(self, fileName): |
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62 self._iWriter = Gff3Writer(fileName) |
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63 |
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64 def setFileName(self, fileName, format): |
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65 chooser = ParserChooser(self._verbosity) |
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66 chooser.findFormat(format) |
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67 self._parser = chooser.getParser(fileName) |
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68 self._sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0]) |
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69 |
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70 def setInterval(self, chromosome, start, end): |
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71 self._chromosome = chromosome |
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72 self._start = start |
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73 self._end = end |
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74 self._transcript = Transcript() |
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75 self._transcript.setChromosome(chromosome) |
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76 self._transcript.setStart(start) |
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77 self._transcript.setEnd(end) |
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78 self._transcript.setDirection("+") |
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79 |
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80 def setTranscript(self, transcript): |
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81 if transcript.__class__.__name__ == "Mapping": |
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82 transcript = transcript.getTranscript() |
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83 self._chromosome = transcript.getChromosome() |
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84 self._start = transcript.getStart() |
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85 self._end = transcript.getEnd() |
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86 self._transcript = transcript |
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87 |
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88 def prepareIntermediateFiles(self): |
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89 fs = FileSorter(self._parser, self._verbosity-4) |
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90 fs.selectChromosome(self._chromosome) |
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91 fs.perChromosome(False) |
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92 fs.setOutputFileName(self._sortedFileName) |
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93 fs.sort() |
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94 self._nbTotalLines = fs.getNbElements() |
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95 self._nbLines = fs.getNbElementsPerChromosome()[self._chromosome] |
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96 |
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97 def createNCList(self): |
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98 if self._verbosity > 2: |
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99 print "Creating NC-list..." |
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100 ncList = NCList(self._verbosity) |
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101 ncList.createIndex(True) |
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102 ncList.setChromosome(self._chromosome) |
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103 ncList.setFileName(self._sortedFileName) |
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104 ncList.setNbElements(self._nbTotalLines) |
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105 ncList.buildLists() |
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106 self.setNCList(ncList, ncList.getIndex()) |
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107 if self._verbosity > 2: |
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108 print " ...done (%ds)" % (endTime - startTime) |
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109 |
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110 def setNCList(self, ncList, index): |
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111 self._ncList = ncList |
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112 self._indix = index |
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113 |
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114 def binarySearch(self, cursor, startL, endL): |
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115 if startL > endL: |
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116 return None |
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117 middleL = (startL + endL) / 2 |
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118 cursor.moveSibling(middleL) |
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119 overlap = self.isOverlapping(cursor) |
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120 if overlap == 0: |
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121 if middleL == startL: |
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122 return cursor |
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123 else: |
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124 return self.binarySearch(cursor, startL, middleL) |
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125 if overlap == -1: |
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126 return self.binarySearch(cursor, middleL + 1, endL) |
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127 return self.binarySearch(cursor, startL, middleL - 1) |
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128 |
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129 def compare(self, cursor = None): |
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130 self._ncList.openFiles() |
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131 if cursor == None: |
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132 dump = True |
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133 cursor = NCListCursor(None, self._ncList, 0, self._verbosity) |
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134 cursor._getSiblingData() |
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135 cursor = self.binarySearch(cursor, cursor._firstSiblingLIndex, cursor._lastSiblingLIndex) |
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136 if cursor == None: |
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137 return |
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138 while not cursor.isOut() and self.isOverlapping(cursor) == 0: |
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139 self.write(cursor) |
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140 newCursor = NCListCursor(cursor) |
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141 if newCursor.hasChildren(): |
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142 newCursor.moveDown() |
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143 self.compare(newCursor) |
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144 if cursor.isLast(): |
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145 return |
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146 cursor.moveRight() |
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147 |
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148 def isOverlapping(self, cursor): |
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149 if self._end < cursor.getStart(): |
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150 return 1 |
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151 if self._start > cursor.getEnd(): |
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152 return -1 |
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153 return 0 |
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154 |
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155 def write(self, cursor): |
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156 self._nbOverlaps += 1 |
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157 refTranscript = cursor.getTranscript() |
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158 self._overlappingNames.append(refTranscript.getName()) |
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159 |
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160 def dumpWriter(self): |
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161 if (not self._overlappingNames) or self._transcript == None: |
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162 return |
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163 self._transcript.setTagValue("nbOverlaps", len(self._overlappingNames)) |
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164 self._transcript.setTagValue("overlapsWith", "--".join(self._overlappingNames)) |
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165 self._iWriter.addTranscript(self._transcript) |
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166 self._nbWritten += 1 |
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167 self._overlappingNames = [] |
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168 |
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169 def run(self): |
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170 self.prepareIntermediateFiles() |
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171 self.createNCList() |
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172 self.compare() |
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173 self.dumpWriter() |
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174 self.close() |
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175 if self._verbosity > 0: |
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176 print "# refs: %d" % (self._nbLines) |
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177 print "# written: %d (%d overlaps)" % (self._nbOverlappingQueries, self._nbOverlaps) |
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178 |
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179 |
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180 if __name__ == "__main__": |
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181 description = "FindOverlapsWithOneInterval: Finds overlaps with one query interval." |
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182 |
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183 parser = OptionParser(description = description) |
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184 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="Input file [compulsory] [format: file in transcript format given by -f]") |
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185 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="Format of previous file [compulsory] [format: transcript file format]") |
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186 parser.add_option("-s", "--start", dest="start", action="store", type="int", help="The start of the query interval [compulsory] [format: int]") |
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187 parser.add_option("-e", "--end", dest="end", action="store", type="int", help="The end of the query interval [compulsory] [format: int]") |
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188 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", type="string", help="Chromosome of the query interval [compulsory] [format: string]") |
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189 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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190 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="Trace level [format: int] [default: 1]") |
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191 (options, args) = parser.parse_args() |
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192 |
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193 iFOWOI = FindOverlapsWithOneInterval(options.verbosity) |
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194 iFOWOI.setFileName(options.inputFileName, options.format) |
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195 iFOWOI.setInterval(options.chromosome, options.start, options.end) |
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196 iFOWOI.setOutputFileName(options.outputFileName) |
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197 iFOWOI.run() |