Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Python/ncList/FileSorter.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 try: |
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33 import cPickle as pickle |
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34 except: |
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35 import pickle |
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36 import random, os |
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37 from heapq import heapify, heappop, heappush |
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38 from itertools import islice, cycle |
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39 from SMART.Java.Python.structure.Transcript import Transcript |
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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 |
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43 BUFFER_SIZE = 100 * 1024 |
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44 |
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45 class FileSorter(object): |
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46 |
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47 def __init__(self, parser, verbosity = 1): |
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48 self._parser = parser |
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49 self._verbosity = verbosity |
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50 self._chunks = {} |
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51 self._nbElements = 0 |
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52 self._nbElementsPerChromosome = {} |
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53 self._perChromosome = False |
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54 self._isPreSorted = False |
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55 self._outputFileNames = {} |
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56 self._prefix = "tmpFile_%d" % (random.randint(0, 100000)) |
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57 self._chromosome = None |
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58 if "SMARTTMPPATH" in os.environ: |
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59 self._prefix = os.path.join(os.environ["SMARTTMPPATH"], self._prefix) |
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60 |
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61 def selectChromosome(self, chromosome): |
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62 self._chromosome = chromosome |
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63 |
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64 def perChromosome(self, boolean): |
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65 self._perChromosome = boolean |
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66 |
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67 def setOutputFileName(self, fileName): |
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68 self._outputFileName = fileName |
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69 if self._perChromosome: |
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70 self._outputFileName = os.path.splitext(self._outputFileName)[0] |
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71 |
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72 def setPresorted(self, presorted): |
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73 self._isPreSorted = presorted |
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74 |
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75 def sort(self): |
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76 if not self._isPreSorted: |
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77 self._batchSort() |
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78 else: |
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79 self._presorted() |
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80 |
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81 def _presorted(self): |
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82 progress = UnlimitedProgress(1000, "Writing files %s" % (self._parser.fileName), self._verbosity) |
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83 curChromosome = None |
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84 outputHandle = None |
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85 |
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86 if not self._perChromosome: |
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87 outputHandle = open(self._outputFileName, "wb") |
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88 for transcript in self._parser.getIterator(): |
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89 progress.inc() |
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90 if transcript.__class__.__name__ == "Mapping": |
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91 transcript = transcript.getTranscript() |
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92 chromosome = transcript.getChromosome() |
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93 if self._chromosome != None and chromosome != self._chromosome: |
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94 continue |
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95 self._nbElements += 1 |
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96 self._nbElementsPerChromosome[chromosome] = self._nbElementsPerChromosome.get(chromosome, 0) + 1 |
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97 if self._perChromosome: |
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98 if chromosome != curChromosome: |
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99 if outputHandle != None: |
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100 outputHandle.close() |
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101 self._outputFileNames[chromosome] = "%s_%s.pkl" % (self._outputFileName, chromosome) |
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102 outputHandle = open(self._outputFileNames[chromosome], "wb") |
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103 curChromosome = chromosome |
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104 outputHandle.writelines("%s" % pickle.dumps(transcript)) |
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105 if outputHandle != None: |
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106 outputHandle.close() |
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107 progress.done() |
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108 |
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109 def getNbElements(self): |
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110 return self._nbElements |
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111 |
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112 def getNbElementsPerChromosome(self): |
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113 return self._nbElementsPerChromosome |
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114 |
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115 def _printSorted(self, chromosome, chunk): |
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116 chunk.sort(key = lambda transcript: (transcript.getStart(), -transcript.getEnd())) |
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117 outputChunk = open("%s_%s_%06i.tmp" % (self._prefix, chromosome, len(self._chunks[chromosome])), "wb", 32000) |
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118 self._chunks[chromosome].append(outputChunk) |
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119 for transcript in chunk: |
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120 outputChunk.write(pickle.dumps(transcript, -1)) |
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121 outputChunk.close() |
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122 |
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123 def _merge(self, chunks): |
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124 values = [] |
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125 for chunk in chunks: |
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126 chunk = open(chunk.name, "rb") |
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127 try: |
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128 transcript = pickle.load(chunk) |
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129 start = transcript.getStart() |
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130 end = -transcript.getEnd() |
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131 except EOFError: |
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132 try: |
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133 chunk.close() |
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134 chunks.remove(chunk) |
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135 os.remove(chunk.name) |
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136 except: |
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137 pass |
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138 else: |
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139 heappush(values, (start, end, transcript, chunk)) |
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140 while values: |
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141 start, end, transcript, chunk = heappop(values) |
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142 yield transcript |
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143 try: |
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144 transcript = pickle.load(chunk) |
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145 start = transcript.getStart() |
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146 end = -transcript.getEnd() |
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147 except EOFError: |
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148 try: |
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149 chunk.close() |
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150 chunks.remove(chunk) |
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151 os.remove(chunk.name) |
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152 except: |
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153 pass |
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154 else: |
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155 heappush(values, (start, end, transcript, chunk)) |
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156 |
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157 def _batchSort(self): |
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158 currentChunks = {} |
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159 counts = {} |
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160 try: |
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161 progress = UnlimitedProgress(1000, "Sorting file %s" % (self._parser.fileName), self._verbosity) |
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162 for transcript in self._parser.getIterator(): |
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163 progress.inc() |
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164 if transcript.__class__.__name__ == "Mapping": |
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165 transcript = transcript.getTranscript() |
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166 chromosome = transcript.getChromosome() |
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167 if self._chromosome != None and chromosome != self._chromosome: |
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168 continue |
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169 if chromosome not in self._chunks: |
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170 self._chunks[chromosome] = [] |
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171 currentChunks[chromosome] = [] |
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172 counts[chromosome] = 0 |
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173 currentChunks[chromosome].append(transcript) |
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174 counts[chromosome] += 1 |
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175 if counts[chromosome] == BUFFER_SIZE: |
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176 self._printSorted(chromosome, currentChunks[chromosome]) |
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177 currentChunks[chromosome] = [] |
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178 counts[chromosome] = 0 |
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179 self._nbElements += 1 |
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180 self._nbElementsPerChromosome[chromosome] = self._nbElementsPerChromosome.get(chromosome, 0) + 1 |
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181 for chromosome in self._chunks: |
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182 if counts[chromosome] > 0: |
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183 self._printSorted(chromosome, currentChunks[chromosome]) |
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184 progress.done() |
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185 if not self._perChromosome: |
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186 outputHandle = open(self._outputFileName, "wb") |
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187 progress = Progress(len(self._chunks), "Writing sorted file %s" % (self._parser.fileName), self._verbosity) |
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188 for chromosome in self._chunks: |
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189 if self._perChromosome: |
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190 self._outputFileNames[chromosome] = "%s_%s.pkl" % (self._outputFileName, chromosome) |
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191 outputHandle = open(self._outputFileNames[chromosome], "wb") |
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192 for sequence in self._merge(self._chunks[chromosome]): |
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193 pickle.dump(sequence, outputHandle, -1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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194 if self._perChromosome: |
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195 outputHandle.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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196 progress.inc() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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197 if not self._perChromosome: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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198 outputHandle.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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199 progress.done() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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200 finally: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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201 for chunks in self._chunks.values(): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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202 for chunk in chunks: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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203 try: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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204 chunk.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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205 os.remove(chunk.name) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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206 except Exception: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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207 pass |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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208 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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209 def getOutputFileNames(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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210 return self._outputFileNames |