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I'm trying to programmatically download files from SRA (with prefetch in sra-tools) starting from a GSE number, using Python.

There is an explanation for using entrez-direct on the CLI, using esearch and the efetch. But I want to use Python. This is what I have now:

from Bio import Entrez
Entrez.email = '[email protected]'
handle = Entrez.esearch(db='gds', query='GSE134195', term="biopython")
record = Entrez.read(handle)

which gives:

record = Entrez.read(handle)
record

{'Count': '17', 'RetMax': '17', 'RetStart': '0', 'IdList': ['200066260', '200045602', '200037064', '200030751', '100013939', '300762998', '300762997', '300762996', '300762995', '300762994', '300762993', '300762992', '300762991', '300762990', '300762989', '300762988', '300762987'], 'TranslationSet': [], 'TranslationStack': [{'Term': 'biopython[All Fields]', 'Field': 'All Fields', 'Count': '17', 'Explode': 'N'}, 'GROUP'], 'QueryTranslation': 'biopython[All Fields]'}

But what are these numbers? IdList looks useful, but there are 17 numbers where I expect 14. How do I get to SRR (SRA) files? The files I want can be found manually here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134195, click on SRA run selector (at the bottom), this bring you here: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA554267, there I can download the Accession list that I want. But I'd like to automate that process.

Thank you in advance.

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  • $\begingroup$ I think thats easy, if I get chance I'll put together a bit of code. $\endgroup$
    – M__ ♦
    Aug 17 at 14:05
  • $\begingroup$ That would be very nice of you, thank you. $\endgroup$
    – Freek
    Aug 17 at 18:09

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