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"/note" feature retrieving through command lines #389
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
Activity
olearyna commentedon Jul 31, 2024
Hi GabrielFalque,
Thank you for opening this issue. We're working with the NCBI Virus Team to include this information in the virus data report. I'll keep this issue open until its implemented.
Nuala
GabrielFalque commentedon Aug 1, 2024
Hi @olearyna ,
Thank you for this. Have a good day.
Gabriel
GabrielFalque commentedon Sep 6, 2024
Hi @olearyna ,
I just wanted to know if it will be implemented soon.
Have a good day.
Gabriel
olearyna commentedon Sep 16, 2024
Hi GabrielFalque,
Sorry for the late reply and thank you for your patience. We currently don't have the data available. We source our data directly from NCBI Virus, and they are still in the process of curating genotype information from the Nucleotide records.
All the best,
Nuala