GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
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Add UnindexedFastaAdapter for fetching small plaintext FASTA files #4531

Closed cmdcolin closed 2 months ago

cmdcolin commented 2 months ago

this allows fetching plaintext FASTA files from remote resources. this allows e.g. fetching a .fasta file without a .fai file from a remote resource

an example of this is for a protein FASTA browser from UniProt

the below screenshot can be generated by fetching https://rest.uniprot.org/uniprotkb/P05067.fasta and https://rest.uniprot.org/uniprotkb/P05067.gff on the fly with no indexing (different tracks are the same gff, with repeated jexlFilters applied)

image

cmdcolin commented 2 months ago

note that this is not wired up to guessAdapter or add-assembly as it's sort of a niche usage...could be added though if we feel it helps