taxon
download a gene dataset by taxon
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 data packages 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 March 11, 2025