taxon

Name

datasets download virus genome taxon - Download a virus genome data package by taxon (NCBI Taxonomy ID, scientific or common name for any virus at any tax rank)

Synopsis

datasets download virus genome taxon <taxon> [flags]

Description

Download a virus genome data package by taxon (NCBI Taxonomy ID, scientific or common name for any virus at any tax rank). Virus genome data packages include genome, transcript and protein sequences, annotation and one or more data reports. Data packages are downloaded as a zip archive.

The default virus genome data package includes the following files:

• genomic.fna (genomic sequences)
• data_report.jsonl (data report with virus genome metadata)
• dataset_catalog.json (a list of files and file types included in the data package)

Examples

  datasets download virus genome taxon sars-cov-2 --host dog --include protein
  datasets download virus genome taxon coronaviridae --host "manis javanica"

Options

      --annotated                 Limit to annotated genomes
      --api-key string            Specify an NCBI API key
      --complete-only             Limit to complete genomes
      --debug                     Emit debugging info
      --filename string           Specify a custom file name for the downloaded data package (default "ncbi_dataset.zip")
      --geo-location string       Limit to genomes isolated from a specified geographic location (continent, country or U.S. state)
      --help                      Print detailed help about a datasets command
      --host string               Limit to virus genomes isolated from a specified host species
      --include string(,string)   Specify virus genome sequence types to download
                                    * genome:     genomic sequences
                                    * cds:        nucleotide coding sequences
                                    * protein:    amino acid sequences
                                    * annotation: annotation report
                                    * biosample:  biosample report
                                    * none:       no sequence data, only primary data report
                                       (default [genome])
      --lineage string            Limit results by Pango lineage (only SARS-CoV-2)
      --no-progressbar            Hide progress bar
      --refseq                    Limit to RefSeq genomes
      --released-after string     Limit to genomes released on or after a specified date (input format is flexible, YYYY/MM/DD is suggested)
      --updated-after string      Limit to genomes updated on or after a specified date (input format is flexible, YYYY/MM/DD is suggested)
      --version                   Print version of datasets