Package ubic.gemma.core.loader.expression.sra

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

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SraFetcher

public SraFetcher(SimpleRetryPolicy retryPolicy,
 @Nullable
 String ncbiApiKey)

Method Details

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