Can we download sequence from the clade level?

[ChongLC]

Dear developer,

I was trying to download protein sequences from the clade level (txid2559587). I was using this code.
python ../../NCBI_Mass_Downloader-5.2/NCBI_downloader.py -q "txid2559587[Organism:exp]" -d "protein" -nv -o C_Ribo21Jul21.fasta

Unfortunately, it shows this error.
"Program finished with some failures.
NCBI returned an error:
{"error":"API rate limit exceeded","api-key":"bbceccfdf97b6b7e06e93c918e010f1ecf09","count":"11","limit":"10"}

Exiting."

Looking forward to hearing from you.

Regards,
CHONG

[StuntsPT]

Dear @ChongLC ,
That is a weird error that I must investigate further.
In order to work around the issue, for a completely working solution, please to the following:
Edit the file back_end.py in your local copy and on line 50, replace the text inside quotes (bbceccfdf97b6b7e06e93c918e010f1ecf09) with your own NCBI API key if you have one.
If you don't have an NCBI API key, you can register for one, or perform another alternative:
Edit your local copy of the file back_end.py and on line 56, replace the value "8" with "6". This will inevitably slow down the downloads, but should allow it to complete.

I'll try to find a proper solution later, so I'll leave your issue open for now.

Best,

Francisco

PS - To answer your question, yes, NCBI_Mass_Sequence_Downloader should work with a clade level txid. At least in theory!

[ChongLC]

Sure, thank you. I will try it out and update you soon.

[ChongLC]

Dear developer,

It looks good after the editing, still running in the current stage. Thank you.

[StuntsPT]

Awesome!
Thank you for your report.