virus-genome

Convert Virus Data Report into TSV format

virus-genome

Convert Virus Data Report into TSV format

Name

dataformat tsv virus-genome - Convert Virus Data Report into TSV format

Synopsis

dataformat tsv virus-genome [flags]

Description

Convert Virus Data Report into TSV format.

Refer to NCBI’s command line start documentation for information about getting started with the command-line tools.

Examples

  dataformat tsv virus-genome --inputfile sars2_package/ncbi_dataset/data/data_report.jsonl
  dataformat tsv virus-genome --package virus-sars2-refseq.zip

Options

      --elide-header       Do not output header
      --fields strings     comma-separated list of fields
  -h, --help               help for virus-genome
      --inputfile string   input file
      --package string     datasets package (zip archive), inputfile parameter is relative to the root path inside the archive

Fields

MnemonicName
accessionAccession
bioprojectsBioProjects
biosample-accBioSample accession
completenessCompleteness
gene-countGene count
geo-locationGeographic location
geo-regionGeographic region
host-common-nameHost Common Name
host-organism-nameHost Organism Name
host-pangolinHost Pangolin Classification
host-strainHost Strain
host-tax-idHost Taxonomic ID
is-annotatedIs Annotated
is-completeIs Complete
isolate-collection-dateIsolate Collection date
isolate-lineageIsolate Lineage
isolate-lineage-sourceIsolate Lineage source
lengthLength
matpeptide-countMature peptide count
mol-typeMolecule type
nucleotide-completenessNucleotide completeness
protein-countProtein count
purpose-of-samplingPurpose of Sampling
release-dateRelease date
sourcedbSource database
sra-accsSRA Accessions
update-dateUpdate date
virus-common-nameVirus Common Name
virus-organism-nameVirus Organism Name
virus-pangolinVirus Pangolin Classification
virus-strainVirus Strain
virus-tax-idVirus Taxonomic ID
Generated October 18, 2021