"/note" feature retrieving through command lines
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 559
- Forks
- 70
- Avg merge
- 1m
- Merged PRs (30d)
- 2
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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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