Mercurial > repos > rmarenco > hubarchivecreator

annotate TrackHub.py @ 1:fb5e60d4d18a draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Wed, 13 Jul 2016 13:36:37 -0400
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children a030b8023882
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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 zipfile
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7 from mako.lookup import TemplateLookup
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10 class TrackHub(object):
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11 """docstring for TrackHub"""
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13 def __init__(self, inputFastaFile, outputFile, extra_files_path, tool_directory):
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14 super(TrackHub, self).__init__()
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16 self.rootAssemblyHub = None
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17 self.mySpecieFolderPath = None
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18 self.tool_directory = tool_directory
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20 # TODO: Modify according to the files passed in parameter
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21 mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')],
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22 output_encoding='utf-8', encoding_errors='replace')
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23 self.trackDbTemplate = mylookup.get_template("layout.txt")
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25 self.extra_files_path = extra_files_path
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26 self.outputFile = outputFile
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28 inputFastaFile = open(inputFastaFile, 'r')
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29 self.outputZip = zipfile.ZipFile(os.path.join(extra_files_path, 'myHub.zip'), 'w')
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31 # Create the structure of the Assembly Hub
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32 # TODO: Merge the following processing into a function as it is also used in twoBitCreator
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33 baseNameFasta = os.path.basename(inputFastaFile.name)
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34 suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
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35 self.twoBitName = suffixTwoBit + '.2bit'
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37 self.rootAssemblyHub = self.__createAssemblyHub__(toolDirectory=tool_directory,
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38 extra_files_path=extra_files_path)
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39
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40 def createZip(self):
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41 for root, dirs, files in os.walk(self.rootAssemblyHub):
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42 # Get all files and construct the dir at the same time
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43 for file in files:
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44 self.outputZip.write(os.path.join(root, file))
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45
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46 self.outputZip.close()
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47
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48 def addTrack(self, trackDbObject=None):
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49 # Create the trackDb.txt file in the specie folder, if not exists
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50 # Else append the new track
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51 trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt')
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52
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53 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
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54 with open(trackDbTxtFilePath, 'a+') as trackDbFile:
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55 trackDbs = [trackDbObject]
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56 htmlMakoRendered = self.trackDbTemplate.render(
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57 trackDbs=trackDbs
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58 )
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59 trackDbFile.write(htmlMakoRendered)
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60
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61 def terminate(self):
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62 # Just a test to output a simple HTML
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63 with open(self.outputFile, 'w') as htmlOutput:
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64 htmlOutput.write('<html>')
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65 htmlOutput.write('<body>')
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66 htmlOutput.write('<p>')
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67 htmlOutput.write('The following generated by Hub Archive Creator:')
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68 htmlOutput.write('</p>')
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69 htmlOutput.write('<ul>')
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70 for root, dirs, files in os.walk(self.extra_files_path):
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71 for file in files:
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72 relDir = os.path.relpath(root, self.extra_files_path)
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73 htmlOutput.write(str.format('<li><a href="{0}">{1}</a></li>', os.path.join(relDir, file),
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74 os.path.join(relDir, file)))
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75 htmlOutput.write('<ul>')
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76 htmlOutput.write('</body>')
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77 htmlOutput.write('</html>')
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78
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79 def __createAssemblyHub__(self, toolDirectory, extra_files_path):
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80 # TODO: Manage to put every fill Function in a file dedicated for reading reasons
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81 # Create the root directory
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82 myHubPath = os.path.join(extra_files_path, "myHub")
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83 if not os.path.exists(myHubPath):
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84 os.makedirs(myHubPath)
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85
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86 # Add the genomes.txt file
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87 genomesTxtFilePath = os.path.join(myHubPath, 'genomes.txt')
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88 self.__fillGenomesTxt__(genomesTxtFilePath, toolDirectory)
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89
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90 # Add the hub.txt file
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91 hubTxtFilePath = os.path.join(myHubPath, 'hub.txt')
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92 self.__fillHubTxt__(hubTxtFilePath, toolDirectory)
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93
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94 # Add the hub.html file
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95 # TODO: Change the name and get it depending on the specie
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96 hubHtmlFilePath = os.path.join(myHubPath, 'dbia.html')
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97 self.__fillHubHtmlFile__(hubHtmlFilePath, toolDirectory)
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98
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99 # Create the specie folder
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100 # TODO: Generate the name depending on the specie
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101 mySpecieFolderPath = os.path.join(myHubPath, "dbia3")
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102 if not os.path.exists(mySpecieFolderPath):
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103 os.makedirs(mySpecieFolderPath)
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104 self.mySpecieFolderPath = mySpecieFolderPath
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105
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106 # Create the description html file in the specie folder
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107 descriptionHtmlFilePath = os.path.join(mySpecieFolderPath, 'description.html')
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108 self.__fillDescriptionHtmlFile__(descriptionHtmlFilePath, toolDirectory)
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109
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110 # Create the file groups.txt
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111 # TODO: If not inputs for this, do no create the file
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112 groupsTxtFilePath = os.path.join(mySpecieFolderPath, 'groups.txt')
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113 self.__fillGroupsTxtFile__(groupsTxtFilePath, toolDirectory)
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114
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115 # Create the folder tracks into the specie folder
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116 tracksFolderPath = os.path.join(mySpecieFolderPath, "tracks")
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117 if not os.path.exists(tracksFolderPath):
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118 os.makedirs(tracksFolderPath)
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119
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120 return myHubPath
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121
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122 def __fillGenomesTxt__(self, genomesTxtFilePath, toolDirectory):
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123 # TODO: Think about the inputs and outputs
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124 # TODO: Manage the template of this file
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125 # renderer = pystache.Renderer(search_dirs="templates/genomesAssembly")
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126 pathTemplate = os.path.join(toolDirectory, 'templates/genomesAssembly')
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127 mylookup = TemplateLookup(directories=[pathTemplate], output_encoding='utf-8', encoding_errors='replace')
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128 mytemplate = mylookup.get_template("layout.txt")
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129 with open(genomesTxtFilePath, 'w') as genomesTxtFile:
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130 # Write the content of the file genomes.txt
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131 twoBitPath = os.path.join('dbia3/', self.twoBitName)
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132 htmlMakoRendered = mytemplate.render(
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133 genomeName="dbia3",
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134 trackDbPath="dbia3/trackDb.txt",
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135 groupsPath="dbia3/groups.txt",
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136 genomeDescription="March 2013 Drosophilia biarmipes unplaced genomic scaffold",
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137 twoBitPath=twoBitPath,
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138 organismName="Drosophilia biarmipes",
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139 defaultPosition="contig1",
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140 orderKey="4500",
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141 scientificName="Drosophilia biarmipes",
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142 pathAssemblyHtmlDescription="dbia3/description.html"
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143 )
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144 genomesTxtFile.write(htmlMakoRendered)
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145
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146 def __fillHubTxt__(self, hubTxtFilePath, toolDirectory):
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147 # TODO: Think about the inputs and outputs
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148 # TODO: Manage the template of this file
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149 mylookup = TemplateLookup(directories=[os.path.join(toolDirectory, 'templates/hubTxt')],
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150 output_encoding='utf-8', encoding_errors='replace')
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151 mytemplate = mylookup.get_template('layout.txt')
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152 with open(hubTxtFilePath, 'w') as genomesTxtFile:
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153 # Write the content of the file genomes.txt
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154 htmlMakoRendered = mytemplate.render(
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155 hubName='dbiaOnly',
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156 shortLabel='dbia',
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157 longLabel='This hub only contains dbia with the gene predictions',
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158 genomesFile='genomes.txt',
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159 email='rmarenco@gwu.edu',
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160 descriptionUrl='dbia.html'
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161 )
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162 genomesTxtFile.write(htmlMakoRendered)
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163
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164 def __fillHubHtmlFile__(self, hubHtmlFilePath, toolDirectory):
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165 # TODO: Think about the inputs and outputs
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166 # TODO: Manage the template of this file
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167 # renderer = pystache.Renderer(search_dirs="templates/hubDescription")
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168 # t = Template(templates.hubDescription.layout.html)
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169 mylookup = TemplateLookup(directories=[os.path.join(toolDirectory, 'templates/hubDescription')],
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170 output_encoding='utf-8', encoding_errors='replace')
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171 mytemplate = mylookup.get_template("layout.txt")
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172 with open(hubHtmlFilePath, 'w') as hubHtmlFile:
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173 # Write the content of the file genomes.txt
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174 # htmlPystached = renderer.render_name(
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175 # "layout",
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176 # {'specie': 'Dbia',
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177 # 'toolUsed': 'Augustus',
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178 # 'ncbiSpecieUrl': 'http://www.ncbi.nlm.nih.gov/genome/3499',
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179 # 'genomeID': '3499',
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180 # 'SpecieFullName': 'Drosophila biarmipes'})
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181 htmlMakoRendered = mytemplate.render(
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182 specie='Dbia',
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183 toolUsed='Augustus',
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184 ncbiSpecieUrl='http://www.ncbi.nlm.nih.gov/genome/3499',
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185 genomeID='3499',
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186 specieFullName='Drosophila biarmipes'
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187 )
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188 # hubHtmlFile.write(htmlPystached)
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189 hubHtmlFile.write(htmlMakoRendered)
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190
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191 def __fillDescriptionHtmlFile__(self, descriptionHtmlFilePath, toolDirectory):
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192 # TODO: Think about the inputs and outputs
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193 # TODO: Manage the template of this file
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194 mylookup = TemplateLookup(directories=[os.path.join(toolDirectory, 'templates/specieDescription')],
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195 output_encoding='utf-8', encoding_errors='replace')
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196 mytemplate = mylookup.get_template("layout.txt")
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197 with open(descriptionHtmlFilePath, 'w') as descriptionHtmlFile:
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198 # Write the content of the file genomes.txt
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199 htmlMakoRendered = mytemplate.render(
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200 specieDescription='This is the description of the dbia',
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201 )
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202 descriptionHtmlFile.write(htmlMakoRendered)
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203
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204 def __fillGroupsTxtFile__(self, groupsTxtFilePath, toolDirectory):
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205 # TODO: Reenable this function at some point
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206 mylookup = TemplateLookup(directories=[os.path.join(toolDirectory, 'templates/groupsTxt')],
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207 output_encoding='utf-8', encoding_errors='replace')
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208 mytemplate = mylookup.get_template("layout.txt")
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209 with open(groupsTxtFilePath, 'w') as groupsTxtFile:
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210 # Write the content of groups.txt
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211 # groupsTxtFile.write('name map')
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212 htmlMakoRendered = mytemplate.render(
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213 mapName='map',
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214 labelMapping='Mapping',
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215 prioriy='2',
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216 isClosed='0'
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217 )
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218 # groupsTxtFile.write(htmlMakoRendered)