gene-id

Name

datasets download ortholog gene-id - download an ortholog dataset by NCBI Gene ID

Synopsis

datasets download ortholog gene-id <gene-id> [flags]

Description

Download an ortholog dataset by NCBI Gene ID. Ortholog data is calculated by NCBI for vertebrates and insects. Ortholog data packages 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 download and install documentation for information about getting started with the command-line tools.

Examples

  datasets download ortholog gene-id 672

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 gene-id
      --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)
  -i, --inputfile string       read a list of NCBI Gene IDs 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