taxon

download a gene dataset by taxon

taxon

download a gene dataset by taxon

Name

datasets download gene taxon - download a gene dataset by taxon

Synopsis

datasets download gene taxon <taxon> [flags]

Description

Download a gene dataset by taxon. 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 taxon human --exclude-gene --exclude-protein --exclude-rna

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 taxon
      --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
Generated October 22, 2021