Mercurial > repos > rmarenco > hubarchivecreator
comparison TrackHub.py @ 11:d05236b15f81 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
| author | rmarenco |
|---|---|
| date | Wed, 27 Jul 2016 10:10:49 -0400 |
| parents | acc233161f50 |
| children | 3233451a3bd6 |
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| 10:acc233161f50 | 11:d05236b15f81 |
|---|---|
| 26 self.tool_directory = tool_directory | 26 self.tool_directory = tool_directory |
| 27 | 27 |
| 28 self.reference_genome = inputFastaFile | 28 self.reference_genome = inputFastaFile |
| 29 # TODO: Add the specie name | 29 # TODO: Add the specie name |
| 30 self.genome_name = inputFastaFile.assembly_id | 30 self.genome_name = inputFastaFile.assembly_id |
| 31 self.specie_html = self.genome_name + '.html' | |
| 31 self.default_pos = None | 32 self.default_pos = None |
| 32 self.user_email = user_email | 33 self.user_email = user_email |
| 33 | 34 |
| 34 # TODO: Modify according to the files passed in parameter | 35 # TODO: Modify according to the files passed in parameter |
| 35 mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')], | 36 mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')], |
| 146 # Add the hub.txt file | 147 # Add the hub.txt file |
| 147 hubTxtFilePath = os.path.join(myHubPath, 'hub.txt') | 148 hubTxtFilePath = os.path.join(myHubPath, 'hub.txt') |
| 148 self.__fillHubTxt__(hubTxtFilePath) | 149 self.__fillHubTxt__(hubTxtFilePath) |
| 149 | 150 |
| 150 # Add the hub.html file | 151 # Add the hub.html file |
| 151 # TODO: Change the name and get it depending on the specie | 152 hubHtmlFilePath = os.path.join(myHubPath, self.specie_html) |
| 152 hubHtmlFilePath = os.path.join(myHubPath, 'dbia.html') | |
| 153 self.__fillHubHtmlFile__(hubHtmlFilePath) | 153 self.__fillHubHtmlFile__(hubHtmlFilePath) |
| 154 | 154 |
| 155 | 155 |
| 156 # Create the description html file in the specie folder | 156 # Create the description html file in the specie folder |
| 157 descriptionHtmlFilePath = os.path.join(mySpecieFolderPath, 'description.html') | 157 descriptionHtmlFilePath = os.path.join(mySpecieFolderPath, 'description.html') |
| 206 hubName=(''.join(['gonramp', self.genome_name.title()])), | 206 hubName=(''.join(['gonramp', self.genome_name.title()])), |
| 207 shortLabel=self.genome_name, | 207 shortLabel=self.genome_name, |
| 208 longLabel=self.genome_name, | 208 longLabel=self.genome_name, |
| 209 genomesFile='genomes.txt', | 209 genomesFile='genomes.txt', |
| 210 email=self.user_email, | 210 email=self.user_email, |
| 211 descriptionUrl='dbia.html' | 211 descriptionUrl=self.specie_html |
| 212 ) | 212 ) |
| 213 genomesTxtFile.write(htmlMakoRendered) | 213 genomesTxtFile.write(htmlMakoRendered) |
| 214 | 214 |
| 215 def __fillHubHtmlFile__(self, hubHtmlFilePath): | 215 def __fillHubHtmlFile__(self, hubHtmlFilePath): |
| 216 # TODO: Think about the inputs and outputs | 216 # TODO: Think about the inputs and outputs |