discrepancies between websearch and pysradb

saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

https://saketkc.github.io/pysradb

BSD 3-Clause "New" or "Revised" License

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discrepancies between websearch and pysradb #50

Closed sebboegel closed 3 years ago

sebboegel commented 4 years ago

Mac OS Cataline 10.15.5 python 3.8 pysradb 0.10.5-dev0

https://www.ncbi.nlm.nih.gov/sra/?term=(rheumatoid+arthritis)+AND+%22Homo+sapiens%22%5Borgn%3A__txid9606%5D yileds 6514 entries

pysradb search -q "rheumatoid arthritis" -m 9000 results in only 287 entries.

What did i wrong?

saketkc commented 4 years ago

Thanks for trying out our experimental feature @sebboegel, appreciate your efforts! I will page in @bscrow who has been working on this.

@bscrow do you know the source of discrepancy?

bscrow commented 4 years ago

Yep it is a bug. I will push a fix in the next update.

Thanks for the bug report!

sebboegel commented 4 years ago

Thank you very much for the fast response and thanks for the tool. It is really valuable. One thing i love is that the output table contains the pmid, which i havent seen in the metadata txt file one can download from SRArunselector.