Get corresponding Biosample accessions for very large list of SRA accesions?

Question

[goatsrunfaster]

I have ~1000 SRR files in a list and I want to get the Biosample accession numbers for each of them without doing it manually. Any easy script to do this sort of thing?

Thanks!

Answer 1

[vkkodali_ncbi]

You can use Entrez Direct for this as follows:

$ esearch -db sra -query 'SRR5437876' | elink -target biosample | efetch 
1: Human sample from Homo sapiens
Identifiers: BioSample: SAMN06710536; Sample name: MCF-7; SRA: SRS2116118
Organism: Homo sapiens
Attributes:
    /isolate="MCF-7"
    /age="69 years"
    /biomaterial provider="missing"
    /sex="female"
    /tissue="breast"
    /cell line="MCF-7 cancer cell line"
Accession: SAMN06710536 ID: 6710536

If you use the -format native -mode xml with the final efetch command, you can get the output in XML format that can be parsed using the xtract command, an Entrez Direct tool.