Mercurial > repos > rmarenco > hubarchivecreator
diff TrackHub.py @ 1:fb5e60d4d18a draft
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 |
| parents | |
| children | a030b8023882 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TrackHub.py Wed Jul 13 13:36:37 2016 -0400 @@ -0,0 +1,218 @@ +#!/usr/bin/python +# -*- coding: utf8 -*- + +import os +import zipfile + +from mako.lookup import TemplateLookup + + +class TrackHub(object): + """docstring for TrackHub""" + + def __init__(self, inputFastaFile, outputFile, extra_files_path, tool_directory): + super(TrackHub, self).__init__() + + self.rootAssemblyHub = None + self.mySpecieFolderPath = None + self.tool_directory = tool_directory + + # TODO: Modify according to the files passed in parameter + mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')], + output_encoding='utf-8', encoding_errors='replace') + self.trackDbTemplate = mylookup.get_template("layout.txt") + + self.extra_files_path = extra_files_path + self.outputFile = outputFile + + inputFastaFile = open(inputFastaFile, 'r') + self.outputZip = zipfile.ZipFile(os.path.join(extra_files_path, 'myHub.zip'), 'w') + + # Create the structure of the Assembly Hub + # TODO: Merge the following processing into a function as it is also used in twoBitCreator + baseNameFasta = os.path.basename(inputFastaFile.name) + suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta) + self.twoBitName = suffixTwoBit + '.2bit' + + self.rootAssemblyHub = self.__createAssemblyHub__(toolDirectory=tool_directory, + extra_files_path=extra_files_path) + + def createZip(self): + for root, dirs, files in os.walk(self.rootAssemblyHub): + # Get all files and construct the dir at the same time + for file in files: + self.outputZip.write(os.path.join(root, file)) + + self.outputZip.close() + + def addTrack(self, trackDbObject=None): + # Create the trackDb.txt file in the specie folder, if not exists + # Else append the new track + trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt') + + # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object + with open(trackDbTxtFilePath, 'a+') as trackDbFile: + trackDbs = [trackDbObject] + htmlMakoRendered = self.trackDbTemplate.render( + trackDbs=trackDbs + ) + trackDbFile.write(htmlMakoRendered) + + def terminate(self): + # Just a test to output a simple HTML + with open(self.outputFile, 'w') as htmlOutput: + htmlOutput.write('<html>') + htmlOutput.write('<body>') + htmlOutput.write('<p>') + htmlOutput.write('The following generated by Hub Archive Creator:') + htmlOutput.write('</p>') + htmlOutput.write('<ul>') + for root, dirs, files in os.walk(self.extra_files_path): + for file in files: + relDir = os.path.relpath(root, self.extra_files_path) + htmlOutput.write(str.format('<li><a href="{0}">{1}</a></li>', os.path.join(relDir, file), + os.path.join(relDir, file))) + htmlOutput.write('<ul>') + htmlOutput.write('</body>') + htmlOutput.write('</html>') + + def __createAssemblyHub__(self, toolDirectory, extra_files_path): + # TODO: Manage to put every fill Function in a file dedicated for reading reasons + # Create the root directory + myHubPath = os.path.join(extra_files_path, "myHub") + if not os.path.exists(myHubPath): + os.makedirs(myHubPath) + + # Add the genomes.txt file + genomesTxtFilePath = os.path.join(myHubPath, 'genomes.txt') + self.__fillGenomesTxt__(genomesTxtFilePath, toolDirectory) + + # Add the hub.txt file + hubTxtFilePath = os.path.join(myHubPath, 'hub.txt') + self.__fillHubTxt__(hubTxtFilePath, toolDirectory) + + # Add the hub.html file + # TODO: Change the name and get it depending on the specie + hubHtmlFilePath = os.path.join(myHubPath, 'dbia.html') + self.__fillHubHtmlFile__(hubHtmlFilePath, toolDirectory) + + # Create the specie folder + # TODO: Generate the name depending on the specie + mySpecieFolderPath = os.path.join(myHubPath, "dbia3") + if not os.path.exists(mySpecieFolderPath): + os.makedirs(mySpecieFolderPath) + self.mySpecieFolderPath = mySpecieFolderPath + + # Create the description html file in the specie folder + descriptionHtmlFilePath = os.path.join(mySpecieFolderPath, 'description.html') + self.__fillDescriptionHtmlFile__(descriptionHtmlFilePath, toolDirectory) + + # Create the file groups.txt + # TODO: If not inputs for this, do no create the file + groupsTxtFilePath = os.path.join(mySpecieFolderPath, 'groups.txt') + self.__fillGroupsTxtFile__(groupsTxtFilePath, toolDirectory) + + # Create the folder tracks into the specie folder + tracksFolderPath = os.path.join(mySpecieFolderPath, "tracks") + if not os.path.exists(tracksFolderPath): + os.makedirs(tracksFolderPath) + + return myHubPath + + def __fillGenomesTxt__(self, genomesTxtFilePath, toolDirectory): + # TODO: Think about the inputs and outputs + # TODO: Manage the template of this file + # renderer = pystache.Renderer(search_dirs="templates/genomesAssembly") + pathTemplate = os.path.join(toolDirectory, 'templates/genomesAssembly') + mylookup = TemplateLookup(directories=[pathTemplate], output_encoding='utf-8', encoding_errors='replace') + mytemplate = mylookup.get_template("layout.txt") + with open(genomesTxtFilePath, 'w') as genomesTxtFile: + # Write the content of the file genomes.txt + twoBitPath = os.path.join('dbia3/', self.twoBitName) + htmlMakoRendered = mytemplate.render( + genomeName="dbia3", + trackDbPath="dbia3/trackDb.txt", + groupsPath="dbia3/groups.txt", + genomeDescription="March 2013 Drosophilia biarmipes unplaced genomic scaffold", + twoBitPath=twoBitPath, + organismName="Drosophilia biarmipes", + defaultPosition="contig1", + orderKey="4500", + scientificName="Drosophilia biarmipes", + pathAssemblyHtmlDescription="dbia3/description.html" + ) + genomesTxtFile.write(htmlMakoRendered) + + def __fillHubTxt__(self, hubTxtFilePath, toolDirectory): + # TODO: Think about the inputs and outputs + # TODO: Manage the template of this file + mylookup = TemplateLookup(directories=[os.path.join(toolDirectory, 'templates/hubTxt')], + output_encoding='utf-8', encoding_errors='replace') + mytemplate = mylookup.get_template('layout.txt') + with open(hubTxtFilePath, 'w') as genomesTxtFile: + # Write the content of the file genomes.txt + htmlMakoRendered = mytemplate.render( + hubName='dbiaOnly', + shortLabel='dbia', + longLabel='This hub only contains dbia with the gene predictions', + genomesFile='genomes.txt', + email='rmarenco@gwu.edu', + descriptionUrl='dbia.html' + ) + genomesTxtFile.write(htmlMakoRendered) + + def __fillHubHtmlFile__(self, hubHtmlFilePath, toolDirectory): + # TODO: Think about the inputs and outputs + # TODO: Manage the template of this file + # renderer = pystache.Renderer(search_dirs="templates/hubDescription") + # t = Template(templates.hubDescription.layout.html) + mylookup = TemplateLookup(directories=[os.path.join(toolDirectory, 'templates/hubDescription')], + output_encoding='utf-8', encoding_errors='replace') + mytemplate = mylookup.get_template("layout.txt") + with open(hubHtmlFilePath, 'w') as hubHtmlFile: + # Write the content of the file genomes.txt + # htmlPystached = renderer.render_name( + # "layout", + # {'specie': 'Dbia', + # 'toolUsed': 'Augustus', + # 'ncbiSpecieUrl': 'http://www.ncbi.nlm.nih.gov/genome/3499', + # 'genomeID': '3499', + # 'SpecieFullName': 'Drosophila biarmipes'}) + htmlMakoRendered = mytemplate.render( + specie='Dbia', + toolUsed='Augustus', + ncbiSpecieUrl='http://www.ncbi.nlm.nih.gov/genome/3499', + genomeID='3499', + specieFullName='Drosophila biarmipes' + ) + # hubHtmlFile.write(htmlPystached) + hubHtmlFile.write(htmlMakoRendered) + + def __fillDescriptionHtmlFile__(self, descriptionHtmlFilePath, toolDirectory): + # TODO: Think about the inputs and outputs + # TODO: Manage the template of this file + mylookup = TemplateLookup(directories=[os.path.join(toolDirectory, 'templates/specieDescription')], + output_encoding='utf-8', encoding_errors='replace') + mytemplate = mylookup.get_template("layout.txt") + with open(descriptionHtmlFilePath, 'w') as descriptionHtmlFile: + # Write the content of the file genomes.txt + htmlMakoRendered = mytemplate.render( + specieDescription='This is the description of the dbia', + ) + descriptionHtmlFile.write(htmlMakoRendered) + + def __fillGroupsTxtFile__(self, groupsTxtFilePath, toolDirectory): + # TODO: Reenable this function at some point + mylookup = TemplateLookup(directories=[os.path.join(toolDirectory, 'templates/groupsTxt')], + output_encoding='utf-8', encoding_errors='replace') + mytemplate = mylookup.get_template("layout.txt") + with open(groupsTxtFilePath, 'w') as groupsTxtFile: + # Write the content of groups.txt + # groupsTxtFile.write('name map') + htmlMakoRendered = mytemplate.render( + mapName='map', + labelMapping='Mapping', + prioriy='2', + isClosed='0' + ) + # groupsTxtFile.write(htmlMakoRendered)