Get all runs for a given bioproject in SRA

NCBI-Hackathons / EDirectCookbook

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Get all runs for a given bioproject in SRA #9

Closed DCGenomics closed 7 years ago

DCGenomics commented 7 years ago

Stuck here so far: esearch -db bioproject -query "PRJNA356464" | elink -target sra | efetch -format docsum

david4096 commented 7 years ago

We made some progress here https://github.com/NCBI-Hackathons/ga4gh-ncbi-api/issues/12 . I think Nic will be able to present a working solution.

DCGenomics commented 7 years ago

Heres a nice way esearch -db bioproject -query "PRJNA356464" | elink -target sra | efetch -format docsum | xtract -pattern DocumentSummary -ACC @acc -block DocumentSummary -element "&ACC"

(thanks to Bob Sanders)