Mercurial > repos > rmarenco > hubarchivecreator

annotate TrackHub.py @ 12:747475757cb0 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 85389def8ed35b3dc08701963dcae4afd1b5b50a
author rmarenco
date Wed, 27 Jul 2016 10:43:58 -0400
parents d05236b15f81
children 3233451a3bd6
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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4 import os
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5 import tempfile
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6 import shutil
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7 import zipfile
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9 # Internal dependencies
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10 from Datatype import Datatype
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11 from util import subtools
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13 from mako.lookup import TemplateLookup
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16 class TrackHub(object):
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17 """docstring for TrackHub"""
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19 def __init__(self, inputFastaFile, user_email, outputFile, extra_files_path, tool_directory):
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20 super(TrackHub, self).__init__()
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22 self.rootAssemblyHub = None
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24 self.mySpecieFolderPath = None
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25 self.myTracksFolderPath = None
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26 self.tool_directory = tool_directory
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28 self.reference_genome = inputFastaFile
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29 # TODO: Add the specie name
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30 self.genome_name = inputFastaFile.assembly_id
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31 self.specie_html = self.genome_name + '.html'
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32 self.default_pos = None
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33 self.user_email = user_email
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35 # TODO: Modify according to the files passed in parameter
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36 mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')],
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37 output_encoding='utf-8', encoding_errors='replace')
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38 self.trackDbTemplate = mylookup.get_template("layout.txt")
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40 self.extra_files_path = extra_files_path
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41 self.outputFile = outputFile
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43 # Create the structure of the Assembly Hub
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44 # TODO: Merge the following processing into a function as it is also used in twoBitCreator
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45 self.twoBitName = None
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46 self.two_bit_final_path = None
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47 self.chromSizesFile = None
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49 self.default_pos = None
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51 # Set all the missing variables of this class, and create physically the folders/files
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52 self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
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54 # Init the Datatype
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55 Datatype.pre_init(self.reference_genome, self.two_bit_final_path, self.chromSizesFile,
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56 self.extra_files_path, self.tool_directory,
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57 self.mySpecieFolderPath, self.myTracksFolderPath)
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59 def createZip(self):
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60 for root, dirs, files in os.walk(self.rootAssemblyHub):
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61 # Get all files and construct the dir at the same time
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62 for file in files:
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63 self.outputZip.write(os.path.join(root, file))
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65 self.outputZip.close()
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67 def addTrack(self, trackDbObject=None):
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68 # Create the trackDb.txt file in the specie folder, if not exists
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69 # Else append the new track
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70 trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt')
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72 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
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73 with open(trackDbTxtFilePath, 'a+') as trackDbFile:
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74 trackDbs = [trackDbObject]
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75 htmlMakoRendered = self.trackDbTemplate.render(
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76 trackDbs=trackDbs
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77 )
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78 trackDbFile.write(htmlMakoRendered)
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80 def terminate(self):
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81 # Just a test to output a simple HTML
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82 # TODO: Create a class to handle the file object
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83 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
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84 output_encoding='utf-8', encoding_errors='replace')
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86 mytemplate = mylookup.get_template('display.txt')
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87 with open(self.outputFile, 'w') as htmlOutput:
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88 # TODO: We are basically looping two times: One time with os.walk, Second time
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89 # with the template. We could improve that if the number of files begins to be really important
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90 list_relative_file_path = [ ]
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91 for root, dirs, files in os.walk(self.extra_files_path):
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92 for file in files:
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93 relative_directory = os.path.relpath(root, self.extra_files_path)
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94 relative_file_path = os.path.join(relative_directory, file)
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95 list_relative_file_path.append(relative_file_path)
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96
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97 htmlMakoRendered = mytemplate.render(
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98 list_relative_file_path=list_relative_file_path
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99 )
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100 htmlOutput.write(htmlMakoRendered)
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101
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102 def __createAssemblyHub__(self, extra_files_path):
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103 # Get all necessaries infos first
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104 # 2bit file creation from input fasta
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105
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106 # baseNameFasta = os.path.basename(fasta_file_name)
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107 # suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
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108 # nameTwoBit = suffixTwoBit + '.2bit'
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109 twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
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110 subtools.faToTwoBit(self.reference_genome.false_path, twoBitFile.name)
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111
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112 # Generate the twoBitInfo
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113 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
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114 subtools.twoBitInfo(twoBitFile.name, twoBitInfoFile.name)
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115
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116 # Then we get the output to generate the chromSizes
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117 self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
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118 subtools.sortChromSizes(twoBitInfoFile.name, self.chromSizesFile.name)
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119
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120 # We can get the biggest scaffold here, with chromSizesFile
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121 with open(self.chromSizesFile.name, 'r') as chrom_sizes:
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122 # TODO: Check if exists
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123 self.default_pos = chrom_sizes.readline().split()[0]
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124
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125 # TODO: Manage to put every fill Function in a file dedicated for reading reasons
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126 # Create the root directory
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127 myHubPath = os.path.join(extra_files_path, "myHub")
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128 if not os.path.exists(myHubPath):
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129 os.makedirs(myHubPath)
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130
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131 # Create the specie folder
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132 # TODO: Generate the name depending on the specie
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133 mySpecieFolderPath = os.path.join(myHubPath, self.genome_name)
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134 if not os.path.exists(mySpecieFolderPath):
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135 os.makedirs(mySpecieFolderPath)
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136 self.mySpecieFolderPath = mySpecieFolderPath
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137
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138 # We create the 2bit file while we just created the specie folder
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139 self.twoBitName = self.genome_name + ".2bit"
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140 self.two_bit_final_path = os.path.join(self.mySpecieFolderPath, self.twoBitName)
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141 shutil.copyfile(twoBitFile.name, self.two_bit_final_path)
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142
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143 # Add the genomes.txt file
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144 genomesTxtFilePath = os.path.join(myHubPath, 'genomes.txt')
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145 self.__fillGenomesTxt__(genomesTxtFilePath)
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146
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147 # Add the hub.txt file
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148 hubTxtFilePath = os.path.join(myHubPath, 'hub.txt')
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149 self.__fillHubTxt__(hubTxtFilePath)
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150
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151 # Add the hub.html file
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152 hubHtmlFilePath = os.path.join(myHubPath, self.specie_html)
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153 self.__fillHubHtmlFile__(hubHtmlFilePath)
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154
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155
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156 # Create the description html file in the specie folder
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157 descriptionHtmlFilePath = os.path.join(mySpecieFolderPath, 'description.html')
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158 self.__fillDescriptionHtmlFile__(descriptionHtmlFilePath)
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159
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160 # Create the file groups.txt
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161 # TODO: If not inputs for this, do no create the file
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162 groupsTxtFilePath = os.path.join(mySpecieFolderPath, 'groups.txt')
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163 self.__fillGroupsTxtFile__(groupsTxtFilePath)
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164
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165 # Create the folder tracks into the specie folder
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166 tracksFolderPath = os.path.join(mySpecieFolderPath, "tracks")
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167 if not os.path.exists(tracksFolderPath):
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168 os.makedirs(tracksFolderPath)
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169 self.myTracksFolderPath = tracksFolderPath
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170
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171 return myHubPath
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172
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173 def __fillGenomesTxt__(self, genomesTxtFilePath):
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174 # TODO: Think about the inputs and outputs
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175 # TODO: Manage the template of this file
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176 # renderer = pystache.Renderer(search_dirs="templates/genomesAssembly")
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177 pathTemplate = os.path.join(self.tool_directory, 'templates/genomesAssembly')
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178 mylookup = TemplateLookup(directories=[pathTemplate], output_encoding='utf-8', encoding_errors='replace')
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179 mytemplate = mylookup.get_template("layout.txt")
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180 with open(genomesTxtFilePath, 'w') as genomesTxtFile:
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181 # Write the content of the file genomes.txt
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182 twoBitPath = os.path.join(self.genome_name, self.twoBitName)
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183 htmlMakoRendered = mytemplate.render(
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184 genomeName=self.genome_name,
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185 trackDbPath=os.path.join(self.genome_name, "trackDb.txt"),
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186 groupsPath=os.path.join(self.genome_name, "groups.txt"),
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187 genomeDescription=self.genome_name,
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188 twoBitPath=twoBitPath,
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189 organismName=self.genome_name,
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190 defaultPosition=self.default_pos,
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191 orderKey="4500",
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192 scientificName=self.genome_name,
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193 pathAssemblyHtmlDescription=os.path.join(self.genome_name, "description.html")
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194 )
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195 genomesTxtFile.write(htmlMakoRendered)
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196
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197 def __fillHubTxt__(self, hubTxtFilePath):
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198 # TODO: Think about the inputs and outputs
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199 # TODO: Manage the template of this file
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200 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/hubTxt')],
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201 output_encoding='utf-8', encoding_errors='replace')
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202 mytemplate = mylookup.get_template('layout.txt')
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203 with open(hubTxtFilePath, 'w') as genomesTxtFile:
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204 # Write the content of the file genomes.txt
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205 htmlMakoRendered = mytemplate.render(
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206 hubName=(''.join(['gonramp', self.genome_name.title()])),
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207 shortLabel=self.genome_name,
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208 longLabel=self.genome_name,
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209 genomesFile='genomes.txt',
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210 email=self.user_email,
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211 descriptionUrl=self.specie_html
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212 )
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213 genomesTxtFile.write(htmlMakoRendered)
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214
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215 def __fillHubHtmlFile__(self, hubHtmlFilePath):
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216 # TODO: Think about the inputs and outputs
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217 # TODO: Manage the template of this file
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218 # renderer = pystache.Renderer(search_dirs="templates/hubDescription")
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219 # t = Template(templates.hubDescription.layout.html)
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220 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/hubDescription')],
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221 output_encoding='utf-8', encoding_errors='replace')
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222 mytemplate = mylookup.get_template("layout.txt")
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223 with open(hubHtmlFilePath, 'w') as hubHtmlFile:
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224 htmlMakoRendered = mytemplate.render(
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225 specie='Dbia',
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226 toolUsed='Augustus',
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227 ncbiSpecieUrl='http://www.ncbi.nlm.nih.gov/genome/3499',
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228 genomeID='3499',
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229 specieFullName='Drosophila biarmipes'
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230 )
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231 #hubHtmlFile.write(htmlMakoRendered)
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232
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233 def __fillDescriptionHtmlFile__(self, descriptionHtmlFilePath):
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234 # TODO: Think about the inputs and outputs
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235 # TODO: Manage the template of this file
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236 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/specieDescription')],
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237 output_encoding='utf-8', encoding_errors='replace')
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238 mytemplate = mylookup.get_template("layout.txt")
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239 with open(descriptionHtmlFilePath, 'w') as descriptionHtmlFile:
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240 # Write the content of the file genomes.txt
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241 htmlMakoRendered = mytemplate.render(
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242 specieDescription='This is the description of the dbia',
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243 )
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244 #descriptionHtmlFile.write(htmlMakoRendered)
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245
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246 def __fillGroupsTxtFile__(self, groupsTxtFilePath):
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247 # TODO: Reenable this function at some point
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248 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/groupsTxt')],
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249 output_encoding='utf-8', encoding_errors='replace')
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250 mytemplate = mylookup.get_template("layout.txt")
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251 with open(groupsTxtFilePath, 'w') as groupsTxtFile:
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252 # Write the content of groups.txt
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253 # groupsTxtFile.write('name map')
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254 htmlMakoRendered = mytemplate.render(
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255 mapName='map',
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256 labelMapping='Mapping',
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257 prioriy='2',
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258 isClosed='0'
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259 )
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260 # groupsTxtFile.write(htmlMakoRendered)