accession
download a gene dataset by RefSeq nucleotide or protein accession
accession
Name
datasets download gene accession - download a gene dataset by RefSeq nucleotide or protein accession
Synopsis
datasets download gene accession <refseq-accession ...> [flags]
Description
Download a gene data package by RefSeq nucleotide or protein accession. Gene data packages include gene, transcript and protein sequence, a data table and a data report. Data packages are downloaded as a zip file.
The default gene data package includes the following files:
- gene.fna (gene sequences)
- rna.fna (transcript sequences)
- protein.faa (protein sequences)
- data_report.jsonl (data report with gene metadata)
- data_table.tsv (data table with gene metadata, one transcript per row)
- dataset_catalog.json (a list of files and file types included in the data package)
- annotation_report.jsonl (included with prokaryotic gene packages)
Refer to NCBI Datasets Gene Package documentation for more information about the gene package.
Examples
datasets download gene accession NP_000483.3
datasets download gene accession NM_000546.6 NM_000492.4
datasets download gene accession WP_004675351.1
Options
--api-key string NCBI Datasets API Key
--exclude-gene exclude gene.fna (gene sequence file)
--exclude-protein exclude protein.faa (protein sequence file)
--exclude-rna exclude rna.fna (transcript sequence file)
--fasta-filter strings limit gene fasta download to a specific list of accessions
--fasta-filter-file string file of accessions to limit gene fasta download
--filename string specify a custom file name for the downloaded dataset (default "ncbi_dataset.zip")
-h, --help help for accession
--include-3p-utr include 3p_utr.fna (3'-UTR sequence file)
--include-5p-utr include 5p_utr.fna (5'-UTR sequence file)
--include-cds include cds.fna (CDS sequence file)
--include-flanks-bp int include gene flanking sequence, limited to prokaryotic genes (default: gene_flanks.fna is omitted from package)
--inputfile string read a list of RefSeq nucleotide or protein accessions from a file to use as input
--no-progressbar hide progress bar
--taxon-filter string limit genes to a specified taxon (any rank)
Generated March 11, 2025