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
Mnemonic | Name |
---|---|
bioproject-accession | BioProjectsAccession |
bioproject-parent-accessions | BioProjectsParent Accessions |
bioproject-title | BioProjectsTitle |
biosample-accession | BioSampleAccession |
description | Description |
genbank-accession | Genbank InformationAccession |
genbank-submission-date | Genbank InformationSubmission Date |
gene-lnc-rna | Gene lncRNA |
gene-protein-coding | Gene Protein-coding |
gene-r-rna | Gene rRNA |
gene-t-rna | Gene tRNA |
gene-total | Gene Total |
organism-common-name | Organism Common Name |
organism-infraspecific-breed | Organism Infraspecific Names Breed |
organism-infraspecific-cultivar | Organism Infraspecific Names Cultivar |
organism-infraspecific-ecotype | Organism Infraspecific Names Ecotype |
organism-infraspecific-isolate | Organism Infraspecific Names Isolate |
organism-infraspecific-sex | Organism Infraspecific Names Sex |
organism-infraspecific-strain | Organism Infraspecific Names Strain |
organism-name | Organism Name |
organism-pangolin | Organism Pangolin Classification |
organism-tax-id | Organism Taxonomic ID |
refseq-accession | RefSeq InformationAccession |
refseq-submission-date | RefSeq InformationSubmission Date |