accession

download an ortholog dataset by RefSeq nucleotide or protein accession

accession

download an ortholog dataset by RefSeq nucleotide or protein accession

Name

datasets download ortholog accession - download an ortholog dataset by RefSeq nucleotide or protein accession

Synopsis

datasets download ortholog accession <refseq-accession> [flags]

Description

Download an ortholog dataset by RefSeq nucleotide or protein accession. Ortholog data is calculated by NCBI for vertebrates and insects. Ortholog datasets include gene, transcript and protein sequence, a data table and a data report. Datasets are downloaded as a zip file.

The default ortholog 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 command line quickstart documentation for information about getting started with the command-line tools.

Examples

  datasets download ortholog accession NP_000483.3
  datasets download ortholog accession NM_000546.6

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)
      --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)
      --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 strings   limit results to ortholog data for a specified taxonomic group
Generated October 18, 2021