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annotate TrackHub.py @ 32:6d1f2bb5c1d1 draft default tip

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5a0c39ed61b4408ba65a759aede807df260d097d
author yating-l
date Sun, 26 Aug 2018 16:44:27 -0400
parents 7e8a8b732db3
children
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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4 import logging
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5 import os
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6 import tempfile
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7 import shutil
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8 import zipfile
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9 from mako.lookup import TemplateLookup
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11 # Internal dependencies
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12 from datatypes.Datatype import Datatype
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13 from util import subtools
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14 from util import santitizer
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19 class TrackHub(object):
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20 """docstring for TrackHub"""
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22 def __init__(self, inputFastaFile, user_email, outputFile, extra_files_path, tool_directory):
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23 super(TrackHub, self).__init__()
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24 self.rootAssemblyHub = None
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26 self.mySpecieFolderPath = None
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27 self.myTracksFolderPath = None
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28 self.tool_directory = tool_directory
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30 self.reference_genome = inputFastaFile
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31 # TODO: Add the specie name
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32 self.genome_name = inputFastaFile.assembly_id
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33 self.specie_html = self.genome_name + '.html'
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34 self.default_pos = None
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35 self.user_email = user_email
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37 # Set containing the groups already added. Updated by addGroup()
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38 self.groups = set()
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40 # TODO: Modify according to the files passed in parameter
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41 # ---- Templates ----
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42 # Template trackDb
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43 mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')],
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44 output_encoding='utf-8', encoding_errors='replace')
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45 self.trackDbTemplate = mylookup.get_template("layout.txt")
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47 # Template groups
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48 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/groupsTxt')],
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49 output_encoding='utf-8', encoding_errors='replace')
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50 self.groupsTemplate = mylookup.get_template("layout.txt")
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52 # ---- End Templates ----
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54 self.extra_files_path = extra_files_path
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55 self.outputFile = outputFile
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57 # Create the structure of the Assembly Hub
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58 # TODO: Merge the following processing into a function as it is also used in twoBitCreator
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59 self.twoBitName = None
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60 self.two_bit_final_path = None
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61 self.chromSizesFile = None
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63 self.default_pos = None
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64
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65 # Set all the missing variables of this class, and create physically the folders/files
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66 self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
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68 # Init the Datatype
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69 Datatype.pre_init(self.reference_genome, self.two_bit_final_path, self.chromSizesFile,
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70 self.extra_files_path, self.tool_directory,
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71 self.mySpecieFolderPath, self.myTracksFolderPath)
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72 '''
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73 def createZip(self):
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74 for root, dirs, files in os.walk(self.rootAssemblyHub):
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75 # Get all files and construct the dir at the same time
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76 for file in files:
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77 self.outputZip.write(os.path.join(root, file))
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79 self.outputZip.close()
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80 '''
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81 def addTrack(self, trackDbObject=None):
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82 # Create the trackDb.txt file in the specie folder, if not exists
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83 # Else append the new track
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84 # TODO: Get this out of the function
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85 trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt')
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86 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
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87 with open(trackDbTxtFilePath, 'a+') as trackDbFile:
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88 group_name = trackDbObject["group"]
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89 trackDbObject["group"] = santitizer.sanitize_group_name(trackDbObject["group"])
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90 trackDbs = [trackDbObject]
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91 # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label
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92 # Add the group as well, if exists in trackDbObject
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93 self.addGroup(group_name)
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94
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95 htmlMakoRendered = self.trackDbTemplate.render(
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96 trackDbs=trackDbs
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97 )
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98 trackDbFile.write(htmlMakoRendered)
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99
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100 #logging.debug("We just added track {0} (in group {1})".format(trackDbObject.trackName,
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101 # trackDbObject.group_name.lower().replace(' ', '_')))
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102 logging.debug("We just added track {0} (in group {1})".format(trackDbObject.get("track"),
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103 trackDbObject.get("group").lower().replace(' ', '_')))
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104 def addGroup(self, group_name="Default"):
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105 # If not already present in self.groups, add to groups.txt
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106 # Create the trackDb.txt file in the specie folder, if not exists
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107 # Else append the new track
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108 # TODO: Get this out of the function
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109 groupsTxtFilePath = os.path.join(self.mySpecieFolderPath, 'groups.txt')
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110
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111 # If the group is already present, we don't need to add it
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112 if group_name in self.groups:
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113 logging.debug("We DON'T add in {0} the group {1}".format(groupsTxtFilePath,
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114 group_name))
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115 return
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116
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117 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
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118 with open(groupsTxtFilePath, 'a+') as groupFile:
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119 # Add the group as well, if exists in trackDbObject
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120
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121 htmlMakoRendered = self.groupsTemplate.render(
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122 label=group_name
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123 )
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124 groupFile.write(htmlMakoRendered)
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125 logging.debug("We just added in {0} the group {1}".format(groupsTxtFilePath,
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126 group_name))
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127 self.groups.add(group_name)
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128
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129 def terminate(self):
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130 # Just a test to output a simple HTML
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131 # TODO: Create a class to handle the file object
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132 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
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133 output_encoding='utf-8', encoding_errors='replace')
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134
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135 mytemplate = mylookup.get_template('display.txt')
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136 with open(self.outputFile, 'w') as htmlOutput:
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137 # TODO: We are basically looping two times: One time with os.walk, Second time
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138 # with the template. We could improve that if the number of files begins to be really important
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139 list_relative_file_path = [ ]
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140
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141 # TODO: Create classes Tree to manage this => Better readibility and maintenability
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142 def create_tree(array_path, tree, relative_array_file_path, level=0):
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143 cur_relative_file_path = '/'.join(relative_array_file_path[:level+1])
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144 if array_path[0] in tree.keys():
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145 create_tree(array_path[1:], tree[array_path[0]][0],
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146 relative_array_file_path, level+1)
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147 else:
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148 tree[array_path[0]] = ({}, cur_relative_file_path)
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149 # TODO: Manage also the links of the directories => No link?
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150 # => Managed in display.txt, but could also be managed there
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151 # If we are don't have any sub-vertices
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152 if len(array_path) == 1:
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153 # We create the path to it
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154 return
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155 else:
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156 create_tree(array_path[1:], tree[array_path[0]][0],
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157 relative_array_file_path, level + 1)
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158
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159 walkable_tree = {}
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160 for root, dirs, files in os.walk(self.extra_files_path):
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161 # Prepare the tree from to perform a Depth First Search
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162 for file in files:
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163 relative_directory = os.path.relpath(root, self.extra_files_path)
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164 relative_file_path = os.path.join(relative_directory, file)
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165 array_path = relative_file_path.split('/')
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166 create_tree(array_path, walkable_tree, array_path, 0)
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167
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168 htmlMakoRendered = mytemplate.render(
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169 walkable_tree=walkable_tree
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170 )
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171 htmlOutput.write(htmlMakoRendered)
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172
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173
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174 def __createAssemblyHub__(self, extra_files_path):
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175 # Get all necessaries infos first
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176 # 2bit file creation from input fasta
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177
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178 # baseNameFasta = os.path.basename(fasta_file_name)
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179 # suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
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180 # nameTwoBit = suffixTwoBit + '.2bit'
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181 twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
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182 subtools.faToTwoBit(self.reference_genome.false_path, twoBitFile.name)
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183
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184 # Generate the twoBitInfo
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185 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
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186 subtools.twoBitInfo(twoBitFile.name, twoBitInfoFile.name)
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187
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188 # Then we get the output to generate the chromSizes
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189 self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
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190 subtools.sortChromSizes(twoBitInfoFile.name, self.chromSizesFile.name)
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191
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192 # We can get the biggest scaffold here, with chromSizesFile
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193 with open(self.chromSizesFile.name, 'r') as chrom_sizes:
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194 # TODO: Check if exists
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195 self.default_pos = chrom_sizes.readline().split()[0]
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196
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197 # TODO: Manage to put every fill Function in a file dedicated for reading reasons
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198 # Create the root directory
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199 myHubPath = os.path.join(extra_files_path, "myHub")
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200 if not os.path.exists(myHubPath):
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201 os.makedirs(myHubPath)
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202
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203 # Create the specie folder
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204 # TODO: Generate the name depending on the specie
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205 mySpecieFolderPath = os.path.join(myHubPath, self.genome_name)
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206 if not os.path.exists(mySpecieFolderPath):
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207 os.makedirs(mySpecieFolderPath)
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208 self.mySpecieFolderPath = mySpecieFolderPath
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209
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210 # We create the 2bit file while we just created the specie folder
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211 self.twoBitName = self.genome_name + ".2bit"
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212 self.two_bit_final_path = os.path.join(self.mySpecieFolderPath, self.twoBitName)
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213 shutil.copyfile(twoBitFile.name, self.two_bit_final_path)
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214
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215 # Add the genomes.txt file
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216 genomesTxtFilePath = os.path.join(myHubPath, 'genomes.txt')
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217 self.__fillGenomesTxt__(genomesTxtFilePath)
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218
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219 # Add the hub.txt file
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220 hubTxtFilePath = os.path.join(myHubPath, 'hub.txt')
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221 self.__fillHubTxt__(hubTxtFilePath)
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222
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223 # Add the hub.html file
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224 hubHtmlFilePath = os.path.join(myHubPath, self.specie_html)
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225 self.__fillHubHtmlFile__(hubHtmlFilePath)
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226
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227
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228 # Create the description html file in the specie folder
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229 descriptionHtmlFilePath = os.path.join(mySpecieFolderPath, 'description.html')
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230 self.__fillDescriptionHtmlFile__(descriptionHtmlFilePath)
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231
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232 # Create the file groups.txt
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233 # TODO: If not inputs for this, do no create the file
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234 # groupsTxtFilePath = os.path.join(mySpecieFolderPath, 'groups.txt')
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235 # self.__fillGroupsTxtFile__(groupsTxtFilePath)
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236
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237 # Create the folder tracks into the specie folder
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238 tracksFolderPath = os.path.join(mySpecieFolderPath, "tracks")
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239 if not os.path.exists(tracksFolderPath):
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240 os.makedirs(tracksFolderPath)
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241 self.myTracksFolderPath = tracksFolderPath
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242
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243 return myHubPath
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244
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245 def __fillGenomesTxt__(self, genomesTxtFilePath):
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246 # TODO: Think about the inputs and outputs
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247 # TODO: Manage the template of this file
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248 # renderer = pystache.Renderer(search_dirs="templates/genomesAssembly")
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249 pathTemplate = os.path.join(self.tool_directory, 'templates/genomesAssembly')
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250 mylookup = TemplateLookup(directories=[pathTemplate], output_encoding='utf-8', encoding_errors='replace')
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251 mytemplate = mylookup.get_template("layout.txt")
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252 with open(genomesTxtFilePath, 'w') as genomesTxtFile:
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253 # Write the content of the file genomes.txt
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254 twoBitPath = os.path.join(self.genome_name, self.twoBitName)
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255 htmlMakoRendered = mytemplate.render(
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256 genomeName=self.genome_name,
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257 trackDbPath=os.path.join(self.genome_name, "trackDb.txt"),
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258 groupsPath=os.path.join(self.genome_name, "groups.txt"),
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259 genomeDescription=self.genome_name,
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260 twoBitPath=twoBitPath,
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261 organismName=self.genome_name,
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262 defaultPosition=self.default_pos,
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263 orderKey="4500",
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264 scientificName=self.genome_name,
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265 pathAssemblyHtmlDescription=os.path.join(self.genome_name, "description.html")
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266 )
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267 genomesTxtFile.write(htmlMakoRendered)
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268
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269 def __fillHubTxt__(self, hubTxtFilePath):
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270 # TODO: Think about the inputs and outputs
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271 # TODO: Manage the template of this file
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272 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/hubTxt')],
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273 output_encoding='utf-8', encoding_errors='replace')
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274 mytemplate = mylookup.get_template('layout.txt')
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275 with open(hubTxtFilePath, 'w') as genomesTxtFile:
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276 # Write the content of the file genomes.txt
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277 htmlMakoRendered = mytemplate.render(
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278 hubName=(''.join(['gonramp', self.genome_name.title()])),
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279 shortLabel=self.genome_name,
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280 longLabel=self.genome_name,
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281 genomesFile='genomes.txt',
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282 email=self.user_email,
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283 descriptionUrl=self.specie_html
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284 )
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285 genomesTxtFile.write(htmlMakoRendered)
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286
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287 def __fillHubHtmlFile__(self, hubHtmlFilePath):
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288 # TODO: Think about the inputs and outputs
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289 # TODO: Manage the template of this file
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290 # renderer = pystache.Renderer(search_dirs="templates/hubDescription")
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291 # t = Template(templates.hubDescription.layout.html)
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292 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/hubDescription')],
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293 output_encoding='utf-8', encoding_errors='replace')
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294 mytemplate = mylookup.get_template("layout.txt")
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295 with open(hubHtmlFilePath, 'w') as hubHtmlFile:
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296 htmlMakoRendered = mytemplate.render(
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297 specie='Dbia',
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298 toolUsed='Augustus',
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299 ncbiSpecieUrl='http://www.ncbi.nlm.nih.gov/genome/3499',
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300 genomeID='3499',
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301 specieFullName='Drosophila biarmipes'
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302 )
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303 #hubHtmlFile.write(htmlMakoRendered)
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304
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305 def __fillDescriptionHtmlFile__(self, descriptionHtmlFilePath):
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306 # TODO: Think about the inputs and outputs
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307 # TODO: Manage the template of this file
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308 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/specieDescription')],
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309 output_encoding='utf-8', encoding_errors='replace')
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310 mytemplate = mylookup.get_template("layout.txt")
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311 with open(descriptionHtmlFilePath, 'w') as descriptionHtmlFile:
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312 # Write the content of the file genomes.txt
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313 htmlMakoRendered = mytemplate.render(
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314 specieDescription='This is the description of the dbia',
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315 )
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316 #descriptionHtmlFile.write(htmlMakoRendered)
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317
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318 def __fillGroupsTxtFile__(self, groupsTxtFilePath):
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319 # TODO: Reenable this function at some point
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320 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/groupsTxt')],
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321 output_encoding='utf-8', encoding_errors='replace')
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322 mytemplate = mylookup.get_template("layout.txt")
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323 with open(groupsTxtFilePath, 'w') as groupsTxtFile:
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324 # Write the content of groups.txt
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325 # groupsTxtFile.write('name map')
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326 htmlMakoRendered = mytemplate.render(
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327 mapName='map',
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328 labelMapping='Mapping',
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329 prioriy='2',
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330 isClosed='0'
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331 )
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332 # groupsTxtFile.write(htmlMakoRendered)