gene

download a gene dataset

Name

datasets download gene - download a gene dataset

Synopsis

datasets download gene [flags]

Description

Download a gene data package including gene, transcript and protein sequence, a data table and a data report. Gene data packages can be specified by NCBI Gene ID, symbol or RefSeq accession. Data packages are downloaded as a zip file.

The default gene dataset 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 dataset)

Refer to NCBI’s download and install documentation for information about getting started with the command-line tools.

Examples

  datasets download gene gene-id 672
  datasets download gene symbol brca1 --taxon mouse
  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             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 gene
      --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)
      --no-progressbar             hide progress bar

Commands


gene-id

download a gene dataset by NCBI Gene ID

symbol

download a gene dataset by gene symbol

accession

download a gene dataset by RefSeq nucleotide or protein accession

taxon

download a gene dataset by taxon

Generated December 6, 2022