taxon

Name

datasets download gene taxon - Download a gene data package by taxon (NCBI Taxonomy ID, scientific or common name for a species)

Synopsis

datasets download gene taxon <taxon> [flags]

Description

Download a gene data package by taxon (NCBI Taxonomy ID, scientific or common name for a species). Gene data packages include gene, transcript and protein sequences and one or more data reports. Data packages are downloaded as a zip archive.

The default gene data package includes the following files:

• rna.fna (transcript sequences)
• protein.faa (protein sequences)
• data_report.jsonl (data report with gene metadata)
• dataset_catalog.json (a list of files and file types included in the data package)

Examples

  datasets download gene taxon human --include protein,cds

Options

      --api-key string             Specify an NCBI API key
      --debug                      Emit debugging info
      --fasta-filter strings       Limit protein and RNA sequence files to the specified RefSeq nucleotide and protein accessions
      --fasta-filter-file string   Limit protein and RNA sequence files to the specified RefSeq nucleotide and protein accessions included in the specified file
      --filename string            Specify a custom file name for the downloaded data package (default "ncbi_dataset.zip")
      --help                       Print detailed help about a datasets command
      --include string(,string)    Specify the data files to include (comma-separated).
                                     * gene:           gene sequence
                                     * rna:            transcript
                                     * protein:        amino acid sequences
                                     * cds:            nucleotide coding sequences
                                     * 5p-utr:         5'-UTR
                                     * 3p-utr:         3'-UTR
                                     * product-report: gene transcript and protein locations and metadata
                                     * none:           do not retrieve any sequence files
                                      (default [rna,protein])
      --no-progressbar             Hide progress bar
      --preview                    Show information about the requested data package
      --version                    Print version of datasets