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 download and install 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
--force Force dataformat to run without type check prompt
-h, --help help for virus-genome
--inputfile string Input file (default "/dev/stdin")
--package string Data package (zip archive), inputfile parameter is relative to the root path inside the archive
Fields
| Mnemonic | Name |
|---|---|
| accession | Accession |
| bioprojects | BioProjects |
| biosample-acc | BioSample accession |
| completeness | Completeness |
| gene-count | Gene count |
| geo-location | Geographic Location |
| geo-region | Geographic Region |
| host-common-name | Host Common Name |
| host-infraspecific-breed | Host Infraspecific Names Breed |
| host-infraspecific-cultivar | Host Infraspecific Names Cultivar |
| host-infraspecific-ecotype | Host Infraspecific Names Ecotype |
| host-infraspecific-isolate | Host Infraspecific Names Isolate |
| host-infraspecific-sex | Host Infraspecific Names Sex |
| host-infraspecific-strain | Host Infraspecific Names Strain |
| host-name | Host Name |
| host-pangolin | Host Pangolin Classification |
| host-tax-id | Host Taxonomic ID |
| is-annotated | Is Annotated |
| is-complete | Is Complete |
| is-lab-host | Is Lab Host |
| is-vaccine-strain | Is Vaccine Strain |
| isolate-collection-date | Isolate Collection date |
| isolate-lineage | Isolate Lineage |
| isolate-lineage-source | Isolate Lineage source |
| lab-host | Lab Host |
| length | Length |
| matpeptide-count | Mature peptide count |
| mol-type | Molecule type |
| nucleotide-completeness | Nucleotide completeness |
| protein-count | Protein count |
| purpose-of-sampling | Purpose of Sampling |
| release-date | Release date |
| sourcedb | Source database |
| sra-accs | SRA Accessions |
| submitter-affiliation | Submitter Affiliation |
| submitter-country | Submitter Country |
| submitter-names | Submitter Names |
| update-date | Update date |
| virus-common-name | Virus Common Name |
| virus-infraspecific-breed | Virus Infraspecific Names Breed |
| virus-infraspecific-cultivar | Virus Infraspecific Names Cultivar |
| virus-infraspecific-ecotype | Virus Infraspecific Names Ecotype |
| virus-infraspecific-isolate | Virus Infraspecific Names Isolate |
| virus-infraspecific-sex | Virus Infraspecific Names Sex |
| virus-infraspecific-strain | Virus Infraspecific Names Strain |
| virus-name | Virus Name |
| virus-pangolin | Virus Pangolin Classification |
| virus-tax-id | Virus Taxonomic ID |