gene

Download a gene data package

Name

datasets download gene - Download a gene data package

Synopsis

datasets download gene [flags]

Description

Download a gene data package. 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 for NM, NR, NP, XM, XR, XP and YP accessions:

  • 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 gene-id 672
  datasets download gene symbol brca1 --taxon "mus musculus"
  datasets download gene accession NP_000483.3
  datasets download gene gene-id 2778 --fasta-filter NC_000020.11,NM_001077490.3,NP_001070958.1

Options

      --api-key string             Specify an NCBI API key
      --debug                      Emit debugging info
      --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])
      --no-progressbar             Hide progress bar
      --preview                    Show information about the requested data package
      --version                    Print version of datasets

Commands


gene-id

Download a gene data package by NCBI Gene ID

symbol

Download a gene data package by gene symbol

accession

Download a gene data package by RefSeq nucleotide or protein accession

taxon

Download a gene data package by taxon (NCBI Taxonomy ID, scientific or common name for a species)

locus-tag

Download a gene data package by locus tag

Generated February 26, 2025