Class SraFetcher
- java.lang.Object
-
- ubic.gemma.core.loader.expression.sra.SraFetcher
-
public class SraFetcher extends Object
-
-
Constructor Summary
Constructors Constructor Description SraFetcher(SimpleRetryPolicy retryPolicy, String ncbiApiKey)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SraExperimentPackageSet
fetch(String accession)
Fetch an SRA experiment.SraExperimentPackageSet
fetchByGeoAccession(String geoAccession)
Fetch an SRA experiment by its GEO association.String
fetchRunInfo(String accession)
Fetch an SRA experiment in the runinfo format.
-
-
-
Constructor Detail
-
SraFetcher
public SraFetcher(SimpleRetryPolicy retryPolicy, @Nullable String ncbiApiKey)
-
-
Method Detail
-
fetch
public SraExperimentPackageSet fetch(String accession) throws IOException
Fetch an SRA experiment.- Throws:
IOException
-
fetchByGeoAccession
public SraExperimentPackageSet fetchByGeoAccession(String geoAccession) throws IOException
Fetch an SRA experiment by its GEO association.This works for GSE and GSM accessions.
- Throws:
IOException
-
fetchRunInfo
public String fetchRunInfo(String accession) throws IOException
Fetch an SRA experiment in the runinfo format.- Throws:
IOException
-
-