public class DownloadManager extends Object
Constructor and Description |
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DownloadManager(CellBaseConfiguration configuration,
Path targetDirectory,
SpeciesConfiguration speciesConfiguration,
SpeciesConfiguration.Assembly assembly) |
Modifier and Type | Method and Description |
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void |
downloadCaddScores() |
void |
downloadClinical() |
void |
downloadConservation()
This method downloads bith PhastCons and PhyloP data from UCSC for Human and Mouse species.
|
void |
downloadEnsemblGene() |
void |
downloadProtein()
This method downloads UniProt, IntAct and Interpro data from EMBL-EBI.
|
void |
downloadReferenceGenome() |
void |
downloadRegulation() |
void |
downloadRepeats() |
void |
downloadStructuralVariants() |
void |
downloadVariation() |
void |
writeDownloadLogFile() |
public DownloadManager(CellBaseConfiguration configuration, Path targetDirectory, SpeciesConfiguration speciesConfiguration, SpeciesConfiguration.Assembly assembly) throws IOException, CellbaseException
IOException
CellbaseException
public void downloadStructuralVariants() throws IOException, InterruptedException
IOException
InterruptedException
public void downloadReferenceGenome() throws IOException, InterruptedException
IOException
InterruptedException
public void downloadEnsemblGene() throws IOException, InterruptedException
IOException
InterruptedException
public void downloadVariation() throws IOException, InterruptedException
IOException
InterruptedException
public void downloadRegulation() throws IOException, InterruptedException
IOException
InterruptedException
public void downloadProtein() throws IOException, InterruptedException
IOException
- if there is an error writing to a fileInterruptedException
- if there is an error downloading filespublic void downloadConservation() throws IOException, InterruptedException
IOException
- if there is an error writing to a fileInterruptedException
- if there is an error downloading filespublic void downloadClinical() throws IOException, InterruptedException
IOException
InterruptedException
public void downloadCaddScores() throws IOException, InterruptedException
IOException
InterruptedException
public void downloadRepeats() throws IOException, InterruptedException
IOException
InterruptedException
public void writeDownloadLogFile() throws IOException
IOException
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