ncbi / ncbi/datasets

"/note" feature retrieving through command lines

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enhancement
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Jupyter Notebook
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Forks
70
Avg merge
1m
Merged PRs (30d)
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Description

I am working on measle disease and want to retrieve metadata from sequenced genomes via the following command :
datasets summary virus genome taxon 11234 --as-json-lines | dataformat tsv virus-genome --fields accession,geo-location,geo-region,virus-infraspecific-strain,virus-name,virus-tax-id,completeness,length,isolate-collection-date,release-date >> mease_metadata.tsv

And one information I need the most is the strain type. But in some numerous cases this information is stored in the following feature (example from MK393364.1 accession number) :

/note="genotype: [B3]"

But I can see that for the moment it is impossible to retrieve this feature, am I wrong ? Or is there another way ?

If not, is it possible for you to add this possibility ?

Thank you in advance.

Gabriel

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Research direction

Start with the shown datasets summary virus genome taxon 11234 --as-json-lines | dataformat tsv virus-genome command and the requested TSV fields. Check whether the /note="genotype: [B3]" feature can be exposed through this command; done means the note or its genotype value can be retrieved for accessions such as MK393364.1.

Written by the indexing model from the issue text.

Assessment

Tech stack
shell
Domain
cli
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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