organelle

Convert Organelle Report into TSV format

organelle

Convert Organelle Report into TSV format

Name

dataformat tsv organelle - Convert Organelle Report into TSV format

Synopsis

dataformat tsv organelle [flags]

Description

Convert Organelle 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 organelle --inputfile organelle_report.jsonl --fields refseq-accession,genbank-accession,'organism*'

Options

      --elide-header       Do not output header
      --fields strings     Comma-separated list of field names that supports wildcards (*). Names with wildcards must be quoted, for example: refseq-accession,genbank-accession,'organism*'
      --force              Force dataformat to run without type check prompt
  -h, --help               help for organelle
      --inputfile string   Input file (default "/dev/stdin")
      --list-templates     List all all available templates for this report type
      --package string     Data package (zip archive), inputfile parameter is relative to the root path inside the archive
      --template string    Pre-defined output format for the current report type

Fields

MnemonicName
bioproject-accessionBioProjectsAccession
bioproject-parent-accessionsBioProjectsParent Accessions
bioproject-titleBioProjectsTitle
biosample-accessionBioSampleAccession
descriptionDescription
genbank-accessionGenbank InformationAccession
genbank-submission-dateGenbank InformationSubmission Date
gene-lnc-rnaGene lncRNA
gene-protein-codingGene Protein-coding
gene-r-rnaGene rRNA
gene-t-rnaGene tRNA
gene-totalGene Total
organism-common-nameOrganism Common Name
organism-infraspecific-breedOrganism Infraspecific Names Breed
organism-infraspecific-cultivarOrganism Infraspecific Names Cultivar
organism-infraspecific-ecotypeOrganism Infraspecific Names Ecotype
organism-infraspecific-isolateOrganism Infraspecific Names Isolate
organism-infraspecific-sexOrganism Infraspecific Names Sex
organism-infraspecific-strainOrganism Infraspecific Names Strain
organism-nameOrganism Name
organism-pangolinOrganism Pangolin Classification
organism-tax-idOrganism Taxonomic ID
refseq-accessionRefSeq InformationAccession
refseq-submission-dateRefSeq InformationSubmission Date
Generated February 26, 2025