locus-tag
Download a gene data package by locus tag
locus-tag
Name
datasets download gene locus-tag - Download a gene data package by locus tag
Synopsis
datasets download gene locus-tag <locus-tag ...> [flags]
Description
Download a gene data package by locus tag. Gene data packages include gene, transcript and protein sequences and one or more data reports. Data packages are downloaded as a zip archive.
The default gene data package includes the following files:
- rna.fna (transcript sequences)
- protein.faa (protein sequences)
- data_report.jsonl (data report with gene metadata)
- dataset_catalog.json (a list of files and file types included in the data package)
Examples
datasets download gene locus-tag b0001
datasets download gene locus-tag b0001 ArthCt125
Options
--api-key string Specify an NCBI API key
--debug Emit debugging info
--fast-zip-validation Skip zip checksum validation after download
--fasta-filter strings Limit protein and RNA sequence files to the specified RefSeq nucleotide and protein accessions
--fasta-filter-file string Limit protein and RNA sequence files to the specified RefSeq nucleotide and protein accessions included in the specified file
--filename string Specify a custom file name for the downloaded data package (default "ncbi_dataset.zip")
--help Print detailed help about a datasets command
--include string(,string) Specify the data files to include (comma-separated).
* gene: gene sequence
* rna: transcript
* protein: amino acid sequences
* cds: nucleotide coding sequences
* 5p-utr: 5'-UTR
* 3p-utr: 3'-UTR
* product-report: gene transcript and protein locations and metadata
* none: do not retrieve any sequence files
(default [rna,protein])
--inputfile string Read a list of NCBI Gene Locus Tags from a file to use as input
--no-progressbar Hide progress bar
--ortholog strings Retrieves data for an ortholog set. Provide one or more taxa (any rank, limited to vertebrates and insects) to filter results or 'all' for the complete set.
--preview Show information about the requested data package
--taxon string Define species (NCBI taxid, common or scientific name) for gene symbol (default "human")
--version Print version of datasets
Generated February 26, 2025