symbol

download a gene dataset by gene symbol

symbol

download a gene dataset by gene symbol

Name

datasets download gene symbol - download a gene dataset by gene symbol

Synopsis

datasets download gene symbol <gene_symbol ...> [flags]

Description

Download a gene dataset by gene symbol and taxon (species name or species-level NCBI Taxonomy ID). If no taxon is specified, data will be returned for human. Gene datasets include gene, transcript and protein sequence, a data table and a data report. Datasets 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 Datasets Gene Package documentation for more information about the gene package.

Examples

  datasets download gene symbol tp53
  datasets download gene symbol brca1 --taxon mouse

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 symbol
      --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)
      --inputfile string           read a list of gene symbols from a file to use as input
      --no-progressbar             hide progress bar
      --taxon string               specify a species name (common or scientific) or species-level NCBI Taxonomy ID (default "human")
Generated October 18, 2021