filter by segmant

[ayana-viritis]

Can you add an option in the dataset API to filter by segment and download (for example download only sequences of Influenza A segment 1)

[olearyna]

Hi ayana-viritis

Thank you for the suggestion. We have added segment filtering to our list of future improvements and we'll update this issue as we make progress.

All the best,

Nuala

[ericcox1]

Hi @ayana-viritis,

In the meantime, you might be interested in the following workaround:

1. Download a highly-compressed, cached package containing all Influenza A virus genome sequences (more information here):
   datasets download virus genome taxon 11320 --filename influenza-a.zip
2. Generate a list of Influenza A segment 1 virus genome accessions using jq:
   unzip -cq influenza-a.zip ncbi_dataset/data/data_report.jsonl | jq 'select(.segment=="1") | .accession' > segment-1.txt
3. Use seqkit grep to copy the segment 1 sequences into a new file:
   unzip -cq influenza-a.zip ncbi_dataset/data/genomic.fna | seqkit grep -f segment-1.txt > segment-1.fna

-Eric

[ayana-viritis]

Thank you very much!

…

________________________________ From: Eric Cox ***@***.***> Sent: Monday, May 11, 2026 11:16 PM To: ncbi/datasets ***@***.***> Cc: Ayana Wiener ***@***.***>; Mention ***@***.***> Subject: Re: [ncbi/datasets] filter by segmant (Issue #578) [https://avatars.githubusercontent.com/u/36059326?s=20&v=4]ericcox1 left a comment (ncbi/datasets#578)<#578 (comment)> Hi @ayana-viritis<https://github.com/ayana-viritis>, In the meantime, you might be interested in the following workaround: 1. Download a highly-compressed, cached package containing all Influenza A virus genome sequences (more information here<https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/virus/get-influenza-genomes/>): datasets download virus genome taxon 11320 --filename influenza-a.zip 2. Generate a list of Influenza A segment 1 virus genome accessions using jq<https://jqlang.org/>: unzip -cq influenza-a.zip ncbi_dataset/data/data_report.jsonl | jq 'select(.segment=="1") | .accession' > segment-1.txt 3. Use seqkit grep<https://bioinf.shenwei.me/seqkit/usage/#grep> to copy the segment 1 sequences into a new file: unzip -cq influenza-a.zip ncbi_dataset/data/genomic.fna | seqkit grep -f segment-1.txt > segment-1.fna

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