Mercurial > repos > rmarenco > hubarchivecreator

annotate TrackHub.py @ 17:c02720d1afee draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author rmarenco
date Fri, 30 Sep 2016 15:14:24 -0400
parents 3233451a3bd6
children d786bca6a75d
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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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10 # Internal dependencies
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11 from Datatype import Datatype
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12 from util import subtools
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14 from mako.lookup import TemplateLookup
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17 class TrackHub(object):
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18 """docstring for TrackHub"""
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20 def __init__(self, inputFastaFile, user_email, outputFile, extra_files_path, tool_directory):
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21 super(TrackHub, self).__init__()
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23 self.rootAssemblyHub = None
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25 self.mySpecieFolderPath = None
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26 self.myTracksFolderPath = None
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27 self.tool_directory = tool_directory
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29 self.reference_genome = inputFastaFile
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30 # TODO: Add the specie name
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31 self.genome_name = inputFastaFile.assembly_id
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32 self.specie_html = self.genome_name + '.html'
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33 self.default_pos = None
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34 self.user_email = user_email
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36 # Set containing the groups already added. Updated by addGroup()
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37 self.groups = set()
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39 # TODO: Modify according to the files passed in parameter
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40 # ---- Templates ----
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41 # Template trackDb
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42 mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')],
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43 output_encoding='utf-8', encoding_errors='replace')
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44 self.trackDbTemplate = mylookup.get_template("layout.txt")
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46 # Template groups
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47 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/groupsTxt')],
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48 output_encoding='utf-8', encoding_errors='replace')
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49 self.groupsTemplate = mylookup.get_template("layout.txt")
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51 # ---- End Templates ----
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53 self.extra_files_path = extra_files_path
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54 self.outputFile = outputFile
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56 # Create the structure of the Assembly Hub
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57 # TODO: Merge the following processing into a function as it is also used in twoBitCreator
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58 self.twoBitName = None
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59 self.two_bit_final_path = None
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60 self.chromSizesFile = None
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62 self.default_pos = None
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64 # Set all the missing variables of this class, and create physically the folders/files
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65 self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
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67 # Init the Datatype
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68 Datatype.pre_init(self.reference_genome, self.two_bit_final_path, self.chromSizesFile,
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69 self.extra_files_path, self.tool_directory,
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70 self.mySpecieFolderPath, self.myTracksFolderPath)
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72 def createZip(self):
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73 for root, dirs, files in os.walk(self.rootAssemblyHub):
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74 # Get all files and construct the dir at the same time
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75 for file in files:
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76 self.outputZip.write(os.path.join(root, file))
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78 self.outputZip.close()
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80 def addTrack(self, trackDbObject=None):
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81 # Create the trackDb.txt file in the specie folder, if not exists
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82 # Else append the new track
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83 # TODO: Get this out of the function
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84 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 trackDbs = [trackDbObject]
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90 # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label
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91 # Add the group as well, if exists in trackDbObject
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92 self.addGroup(trackDbObject.group_name)
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93
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94 htmlMakoRendered = self.trackDbTemplate.render(
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95 trackDbs=trackDbs
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96 )
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97 trackDbFile.write(htmlMakoRendered)
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98
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99 def addGroup(self, group_name="Default"):
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100 # If not already present in self.groups, add to groups.txt
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101 # Create the trackDb.txt file in the specie folder, if not exists
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102 # Else append the new track
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103 # TODO: Get this out of the function
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104 groupsTxtFilePath = os.path.join(self.mySpecieFolderPath, 'groups.txt')
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105
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106 # If the group is already present, we don't need to add it
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107 if group_name in self.groups:
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108 return
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109
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110 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
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111 with open(groupsTxtFilePath, 'a+') as groupFile:
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112 # Add the group as well, if exists in trackDbObject
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113
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114 htmlMakoRendered = self.groupsTemplate.render(
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115 label=group_name
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116 )
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117 groupFile.write(htmlMakoRendered)
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118 self.groups.add(group_name)
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119
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120 def terminate(self):
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121 # Just a test to output a simple HTML
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122 # TODO: Create a class to handle the file object
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123 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
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124 output_encoding='utf-8', encoding_errors='replace')
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125
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126 mytemplate = mylookup.get_template('display.txt')
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127 with open(self.outputFile, 'w') as htmlOutput:
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128 # TODO: We are basically looping two times: One time with os.walk, Second time
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129 # with the template. We could improve that if the number of files begins to be really important
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130 list_relative_file_path = [ ]
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131
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132 # TODO: Create classes Tree to manage this => Better readibility and maintenability
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133 def create_tree(array_path, tree, relative_array_file_path, level=0):
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134 cur_relative_file_path = '/'.join(relative_array_file_path[:level+1])
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135 if array_path[0] in tree.keys():
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136 create_tree(array_path[1:], tree[array_path[0]][0],
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137 relative_array_file_path, level+1)
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138 else:
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139 tree[array_path[0]] = ({}, cur_relative_file_path)
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140 # TODO: Manage also the links of the directories => No link?
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141 # => Managed in display.txt, but could also be managed there
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142 # If we are don't have any sub-vertices
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143 if len(array_path) == 1:
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144 # We create the path to it
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145 return
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146 else:
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147 create_tree(array_path[1:], tree[array_path[0]][0],
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148 relative_array_file_path, level + 1)
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149
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150 walkable_tree = {}
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151 for root, dirs, files in os.walk(self.extra_files_path):
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152 # Prepare the tree from to perform a Depth First Search
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153 for file in files:
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154 relative_directory = os.path.relpath(root, self.extra_files_path)
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155 relative_file_path = os.path.join(relative_directory, file)
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156 array_path = relative_file_path.split('/')
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157 create_tree(array_path, walkable_tree, array_path, 0)
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158
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159 htmlMakoRendered = mytemplate.render(
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160 walkable_tree=walkable_tree
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161 )
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162 htmlOutput.write(htmlMakoRendered)
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163
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164 def __createAssemblyHub__(self, extra_files_path):
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165 # Get all necessaries infos first
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166 # 2bit file creation from input fasta
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167
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168 # baseNameFasta = os.path.basename(fasta_file_name)
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169 # suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
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170 # nameTwoBit = suffixTwoBit + '.2bit'
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171 twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
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172 subtools.faToTwoBit(self.reference_genome.false_path, twoBitFile.name)
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173
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174 # Generate the twoBitInfo
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175 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
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176 subtools.twoBitInfo(twoBitFile.name, twoBitInfoFile.name)
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177
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178 # Then we get the output to generate the chromSizes
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179 self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
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180 subtools.sortChromSizes(twoBitInfoFile.name, self.chromSizesFile.name)
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181
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182 # We can get the biggest scaffold here, with chromSizesFile
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183 with open(self.chromSizesFile.name, 'r') as chrom_sizes:
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184 # TODO: Check if exists
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185 self.default_pos = chrom_sizes.readline().split()[0]
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186
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187 # TODO: Manage to put every fill Function in a file dedicated for reading reasons
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188 # Create the root directory
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189 myHubPath = os.path.join(extra_files_path, "myHub")
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190 if not os.path.exists(myHubPath):
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191 os.makedirs(myHubPath)
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192
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193 # Create the specie folder
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194 # TODO: Generate the name depending on the specie
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195 mySpecieFolderPath = os.path.join(myHubPath, self.genome_name)
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196 if not os.path.exists(mySpecieFolderPath):
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197 os.makedirs(mySpecieFolderPath)
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198 self.mySpecieFolderPath = mySpecieFolderPath
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199
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200 # We create the 2bit file while we just created the specie folder
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201 self.twoBitName = self.genome_name + ".2bit"
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202 self.two_bit_final_path = os.path.join(self.mySpecieFolderPath, self.twoBitName)
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203 shutil.copyfile(twoBitFile.name, self.two_bit_final_path)
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204
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205 # Add the genomes.txt file
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206 genomesTxtFilePath = os.path.join(myHubPath, 'genomes.txt')
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207 self.__fillGenomesTxt__(genomesTxtFilePath)
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208
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209 # Add the hub.txt file
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210 hubTxtFilePath = os.path.join(myHubPath, 'hub.txt')
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211 self.__fillHubTxt__(hubTxtFilePath)
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212
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213 # Add the hub.html file
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214 hubHtmlFilePath = os.path.join(myHubPath, self.specie_html)
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215 self.__fillHubHtmlFile__(hubHtmlFilePath)
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216
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217
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218 # Create the description html file in the specie folder
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219 descriptionHtmlFilePath = os.path.join(mySpecieFolderPath, 'description.html')
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220 self.__fillDescriptionHtmlFile__(descriptionHtmlFilePath)
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221
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222 # Create the file groups.txt
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223 # TODO: If not inputs for this, do no create the file
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224 # groupsTxtFilePath = os.path.join(mySpecieFolderPath, 'groups.txt')
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225 # self.__fillGroupsTxtFile__(groupsTxtFilePath)
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226
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227 # Create the folder tracks into the specie folder
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228 tracksFolderPath = os.path.join(mySpecieFolderPath, "tracks")
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229 if not os.path.exists(tracksFolderPath):
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230 os.makedirs(tracksFolderPath)
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231 self.myTracksFolderPath = tracksFolderPath
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232
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233 return myHubPath
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234
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235 def __fillGenomesTxt__(self, genomesTxtFilePath):
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236 # TODO: Think about the inputs and outputs
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237 # TODO: Manage the template of this file
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238 # renderer = pystache.Renderer(search_dirs="templates/genomesAssembly")
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239 pathTemplate = os.path.join(self.tool_directory, 'templates/genomesAssembly')
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240 mylookup = TemplateLookup(directories=[pathTemplate], output_encoding='utf-8', encoding_errors='replace')
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241 mytemplate = mylookup.get_template("layout.txt")
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242 with open(genomesTxtFilePath, 'w') as genomesTxtFile:
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243 # Write the content of the file genomes.txt
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244 twoBitPath = os.path.join(self.genome_name, self.twoBitName)
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245 htmlMakoRendered = mytemplate.render(
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246 genomeName=self.genome_name,
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247 trackDbPath=os.path.join(self.genome_name, "trackDb.txt"),
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248 groupsPath=os.path.join(self.genome_name, "groups.txt"),
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249 genomeDescription=self.genome_name,
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250 twoBitPath=twoBitPath,
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251 organismName=self.genome_name,
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252 defaultPosition=self.default_pos,
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253 orderKey="4500",
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254 scientificName=self.genome_name,
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255 pathAssemblyHtmlDescription=os.path.join(self.genome_name, "description.html")
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256 )
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257 genomesTxtFile.write(htmlMakoRendered)
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258
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259 def __fillHubTxt__(self, hubTxtFilePath):
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260 # TODO: Think about the inputs and outputs
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261 # TODO: Manage the template of this file
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262 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/hubTxt')],
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263 output_encoding='utf-8', encoding_errors='replace')
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264 mytemplate = mylookup.get_template('layout.txt')
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265 with open(hubTxtFilePath, 'w') as genomesTxtFile:
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266 # Write the content of the file genomes.txt
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267 htmlMakoRendered = mytemplate.render(
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268 hubName=(''.join(['gonramp', self.genome_name.title()])),
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269 shortLabel=self.genome_name,
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270 longLabel=self.genome_name,
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271 genomesFile='genomes.txt',
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272 email=self.user_email,
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273 descriptionUrl=self.specie_html
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274 )
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275 genomesTxtFile.write(htmlMakoRendered)
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276
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277 def __fillHubHtmlFile__(self, hubHtmlFilePath):
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278 # TODO: Think about the inputs and outputs
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279 # TODO: Manage the template of this file
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280 # renderer = pystache.Renderer(search_dirs="templates/hubDescription")
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281 # t = Template(templates.hubDescription.layout.html)
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282 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/hubDescription')],
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283 output_encoding='utf-8', encoding_errors='replace')
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284 mytemplate = mylookup.get_template("layout.txt")
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285 with open(hubHtmlFilePath, 'w') as hubHtmlFile:
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286 htmlMakoRendered = mytemplate.render(
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287 specie='Dbia',
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288 toolUsed='Augustus',
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289 ncbiSpecieUrl='http://www.ncbi.nlm.nih.gov/genome/3499',
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290 genomeID='3499',
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291 specieFullName='Drosophila biarmipes'
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292 )
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293 #hubHtmlFile.write(htmlMakoRendered)
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294
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295 def __fillDescriptionHtmlFile__(self, descriptionHtmlFilePath):
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296 # TODO: Think about the inputs and outputs
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297 # TODO: Manage the template of this file
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298 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/specieDescription')],
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299 output_encoding='utf-8', encoding_errors='replace')
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300 mytemplate = mylookup.get_template("layout.txt")
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301 with open(descriptionHtmlFilePath, 'w') as descriptionHtmlFile:
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302 # Write the content of the file genomes.txt
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303 htmlMakoRendered = mytemplate.render(
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304 specieDescription='This is the description of the dbia',
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305 )
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306 #descriptionHtmlFile.write(htmlMakoRendered)
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307
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308 def __fillGroupsTxtFile__(self, groupsTxtFilePath):
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309 # TODO: Reenable this function at some point
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310 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/groupsTxt')],
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311 output_encoding='utf-8', encoding_errors='replace')
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312 mytemplate = mylookup.get_template("layout.txt")
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313 with open(groupsTxtFilePath, 'w') as groupsTxtFile:
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314 # Write the content of groups.txt
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315 # groupsTxtFile.write('name map')
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316 htmlMakoRendered = mytemplate.render(
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317 mapName='map',
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318 labelMapping='Mapping',
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319 prioriy='2',
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320 isClosed='0'
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321 )
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322 # groupsTxtFile.write(htmlMakoRendered)