Mercurial > repos > yating-l > jbrowsearchivecreator

annotate TrackHub.py @ 38:d17f629f5486 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
author yating-l
date Fri, 06 Apr 2018 13:44:56 -0400
parents 07cc5384dd61
children 4a69515eed63
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1 #!/usr/bin/env python
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3 import os
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4 import subprocess
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5 import shutil
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6 import zipfile
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7 import json
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8 import tempfile
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9 import logging
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10 from mako.lookup import TemplateLookup
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12 from datatypes.Datatype import Datatype
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13 from tracks.TrackStyles import TrackStyles
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14 from util import subtools
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15 from util import santitizer
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18 class TrackHub:
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19 def __init__(self, inputFastaFile, outputFile, extra_files_path, tool_directory, trackType):
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21 self.rootAssemblyHub = None
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23 self.mySpecieFolderPath = None
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25 # Store intermediate files, will be removed if not in debug mode
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26 self.myTracksFolderPath = None
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28 # Store binary files: Bam, BigWig
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29 self.myBinaryFolderPath = None
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31 self.tool_directory = tool_directory
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32 self.trackType = trackType
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33 self.reference_genome = inputFastaFile
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34 self.genome_name = inputFastaFile.assembly_id
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35 self.extra_files_path = extra_files_path
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36 self.outputFile = outputFile
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37 self.chromSizesFile = None
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40 # Set all the missing variables of this class, and create physically the folders/files
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41 self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
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42 # Init the Datatype
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43 Datatype.pre_init(self.reference_genome, self.chromSizesFile,
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44 self.extra_files_path, self.tool_directory,
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45 self.mySpecieFolderPath, self.myTracksFolderPath, self.myFinalTracksFolderPath, self.myBinaryFolderPath, self.trackType)
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47 self._prepareRefseq()
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48 self.trackList = os.path.join(self.mySpecieFolderPath, "trackList.json")
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49 self._createTrackList()
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51 self.myTrackStyle = TrackStyles(self.tool_directory, self.mySpecieFolderPath, self.trackList)
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52 #self.cssFolderPath = os.path.join(self.mySpecieFolderPath, 'css')
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53 #self.cssFilePath = os.path.join(self.cssFolderPath, 'custom_track_styles.css')
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54 self.logger = logging.getLogger(__name__)
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55
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56
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58 def addTrack(self, trackDbObject):
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59 if trackDbObject['dataType'].lower() == 'bam':
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60 #new_track = subprocess.Popen(['echo', trackDbObject['options']], stdout=subprocess.PIPE)
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61 #subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
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62 subtools.add_track_json(self.trackList, trackDbObject['options'])
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63 #subtools.add_track_json(self.trackList, trackDbObject['track_json'])
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64 elif trackDbObject['dataType'].lower() == 'bigwig':
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65 subtools.add_track_json(self.trackList, trackDbObject['options'])
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66 else:
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67 if trackDbObject['trackType'] == 'HTMLFeatures':
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68 self._customizeHTMLFeature(trackDbObject)
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69 subtools.flatfile_to_json(trackDbObject['trackDataURL'], trackDbObject['dataType'], trackDbObject['trackType'], trackDbObject['trackLabel'], self.mySpecieFolderPath, trackDbObject['options'])
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70 # Use Tabix index tracks by default for CanvasFeatures
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71 # TODO: add support for HTMLFeatures
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72 else:
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73 subtools.generate_tabix_indexed_track(trackDbObject['trackDataURL'], trackDbObject['dataType'], self.myFinalTracksFolderPath)
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74 subtools.add_track_json(self.trackList, trackDbObject['options'])
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76 def terminate(self, debug=False):
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77 """ Write html file """
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78 self._indexName()
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79 if not debug:
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80 self._removeRaw()
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81 #self._makeArchive()
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82 self._outHtml()
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83 print "Success!\n"
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86 def _customizeHTMLFeature(self, trackDbObject):
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87 if trackDbObject['options']:
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88 subfeatures = trackDbObject['options'].get('subfeatureClasses')
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89 feature_color = trackDbObject['options']['feature_color']
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90 if subfeatures:
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91 for key, value in subfeatures.items():
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92 self.myTrackStyle.addCustomColor(value, feature_color)
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93 else:
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94 customizedFeature = santitizer.sanitize_name(trackDbObject['trackLabel'])
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95 clientConfig = json.loads(trackDbObject['options']['clientConfig'])
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96 clientConfig['renderClassName'] = customizedFeature
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97 trackDbObject['options']['clientConfig'] = json.dumps(clientConfig)
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98 self.myTrackStyle.addCustomColor(customizedFeature, feature_color)
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99
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100 def _removeRaw(self):
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101 if os.path.exists(self.myTracksFolderPath):
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102 shutil.rmtree(self.myTracksFolderPath)
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103
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104 def _createTrackList(self):
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105 if not os.path.exists(self.trackList):
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106 os.mknod(self.trackList)
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107
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108 def _prepareRefseq(self):
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109 subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
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110 #try:
0
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111 #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
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112 #subprocess.call(['prepare-refseqs.pl', '--fasta', self.reference_genome.false_path, '--out', self.mySpecieFolderPath])
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113 #except OSError as e:
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114 #print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
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115
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116 def _indexName(self):
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117 #subprocess.call(['generate-names.pl', '-v', '--out', self.mySpecieFolderPath])
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118 subtools.generate_names(self.mySpecieFolderPath)
0
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119 print "finished name index \n"
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120
32
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121 def _outHtml(self):
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122 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
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123 output_encoding='utf-8', encoding_errors='replace')
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124 htmlTemplate = mylookup.get_template("display.txt")
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125
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126 with open(self.outputFile, 'w') as htmlfile:
32
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127 htmlMakoRendered = htmlTemplate.render(
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128 species_folder = os.path.relpath(self.mySpecieFolderPath, self.extra_files_path),
32
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129 trackList = os.path.relpath(self.trackList, self.extra_files_path)
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130 )
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131 htmlfile.write(htmlMakoRendered)
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132 #with open(self.outputFile, 'w') as htmlfile:
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133 # htmlstr = 'The new Organism "%s" is created on Apollo: <br>' % self.genome_name
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134 # jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
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135 # htmlstr += jbrowse_hub
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136 # htmlfile.write(htmlstr)
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137
25
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138
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139
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140 def __createAssemblyHub__(self, extra_files_path):
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141 # Get all necessaries infos first
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142 # 2bit file creation from input fasta
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143
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144 # baseNameFasta = os.path.basename(fasta_file_name)
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145 # suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
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146 # nameTwoBit = suffixTwoBit + '.2bit'
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147 twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
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148 subtools.faToTwoBit(self.reference_genome.false_path, twoBitFile.name)
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149
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150 # Generate the twoBitInfo
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151 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
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152 subtools.twoBitInfo(twoBitFile.name, twoBitInfoFile.name)
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153
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154 # Then we get the output to generate the chromSizes
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155 self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
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156 subtools.sortChromSizes(twoBitInfoFile.name, self.chromSizesFile.name)
0
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157
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158 # We can get the biggest scaffold here, with chromSizesFile
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159 with open(self.chromSizesFile.name, 'r') as chrom_sizes:
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160 # TODO: Check if exists
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161 self.default_pos = chrom_sizes.readline().split()[0]
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162
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163 # TODO: Manage to put every fill Function in a file dedicated for reading reasons
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164 # Create the root directory
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165 myHubPath = os.path.join(extra_files_path, "myHub")
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166 if not os.path.exists(myHubPath):
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167 os.makedirs(myHubPath)
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168
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169 # Create the specie folder
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170 mySpecieFolderPath = os.path.join(myHubPath, self.genome_name)
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171 if not os.path.exists(mySpecieFolderPath):
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172 os.makedirs(mySpecieFolderPath)
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173 self.mySpecieFolderPath = mySpecieFolderPath
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174
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175 # Create the folder named 'raw' inside the specie folder to place raw files
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176 tracksFolderPath = os.path.join(mySpecieFolderPath, "raw")
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177 if not os.path.exists(tracksFolderPath):
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178 os.makedirs(tracksFolderPath)
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179 self.myTracksFolderPath = tracksFolderPath
0
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180
38
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181 # Create the folder tracks into the specie folder
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182 finalTracksFolderPath = os.path.join(mySpecieFolderPath, "tracks")
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183 if not os.path.exists(finalTracksFolderPath):
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184 os.makedirs(finalTracksFolderPath)
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185 self.myFinalTracksFolderPath = finalTracksFolderPath
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186
25
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187 myBinaryFolderPath = os.path.join(mySpecieFolderPath, 'bbi')
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188 if not os.path.exists(myBinaryFolderPath):
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189 os.makedirs(myBinaryFolderPath)
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190 self.myBinaryFolderPath = myBinaryFolderPath
0
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191
25
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192 return myHubPath