`ffq` does not work for some low-number SRRs

[jbloom]

I'm not sure if this is expected behavior, but ffq does not work for some low-number SRRs. For instance, ffq SRR038165 gives

[2021-07-23 06:33:59,377]    INFO Parsing run SRR038165
[2021-07-23 06:34:02,904]   ERROR 400 Client Error:  for url: https://www.ebi.ac.uk/ena/browser/api/xml/SRS011879,SRS024956-SRS025194/

despite the fact that SRR038165 is a valid SRR: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR038165

[agalvezm]

Hello! Our apologies for the delay in the response. I looked into the error and it does not seem to be caused by the fact that it is a low-number SRR. Instead, the error arises because there are multiple SRS ids that are associated with that SRR. We have fixed this issue and made lots of improvements to ffq in the devel branch of the repository, which will be merged with master soon. We have also implemented different test cases to make the tool more robust and avoid this sort of issues. Thanks so much for using ffq and feel free to ask any other questions you may have! :)

[sbooeshaghi]

Hi @jbloom this issue has been fixed and merged into the master branch. An updated version of ffq can be install with

pip install git+https://github.com/pachterlab/ffq

and the accession can be fetched with

ffq SRR038165

We plan on creating an official release (and updating the package on pip) soon. Thank you for bringing this accession to our attention!