gene

Convert Gene Report into TSV format

Contents

gene

Convert Gene Report into TSV format

Name

dataformat tsv gene - Convert Gene Report into TSV format

Synopsis

dataformat tsv gene [flags]

Description

Convert Gene 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 gene --inputfile gene_package/ncbi_dataset/data/data_report.jsonl
  dataformat tsv gene --package genes.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 gene
      --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
annotation-assembly-accession	Annotation Assembly Accession
annotation-assembly-name	Annotation Assembly Name
annotation-genomic-range-accession	Annotation Genomic Range Accession
annotation-genomic-range-exon-order	Annotation Genomic Range Exons Order
annotation-genomic-range-exon-orientation	Annotation Genomic Range Exons Orientation
annotation-genomic-range-exon-start	Annotation Genomic Range Exons Start
annotation-genomic-range-exon-stop	Annotation Genomic Range Exons Stop
annotation-genomic-range-range-order	Annotation Genomic Range Order
annotation-genomic-range-range-orientation	Annotation Genomic Range Orientation
annotation-genomic-range-range-start	Annotation Genomic Range Start
annotation-genomic-range-range-stop	Annotation Genomic Range Stop
annotation-genomic-range-seq-name	Annotation Genomic Range Seq Name
annotation-release-date	Annotation Release Date
annotation-release-name	Annotation Release Name
chromosomes	Chromosomes
common-name	Common Name
description	Description
ensembl-geneids	Ensembl GeneIDs
gene-id	NCBI GeneID
gene-type	Gene Type
genomic-region-gene-range-accession	Genomic Region Gene Range Sequence Accession
genomic-region-gene-range-range-order	Genomic Region Gene Range Order
genomic-region-gene-range-range-orientation	Genomic Region Gene Range Orientation
genomic-region-gene-range-range-start	Genomic Region Gene Range Start
genomic-region-gene-range-range-stop	Genomic Region Gene Range Stop
genomic-region-genomic-region-type	Genomic Region Genomic Region Type
group-id	Gene Group Identifier
group-method	Gene Group Method
name-authority	Nomenclature Authority
name-id	Nomenclature ID
omim-ids	OMIM IDs
orientation	Orientation
protein-count	Proteins
ref-standard-gene-range-accession	Reference Standard Gene Range Sequence Accession
ref-standard-gene-range-range-order	Reference Standard Gene Range Order
ref-standard-gene-range-range-orientation	Reference Standard Gene Range Orientation
ref-standard-gene-range-range-start	Reference Standard Gene Range Start
ref-standard-gene-range-range-stop	Reference Standard Gene Range Stop
ref-standard-genomic-region-type	Reference Standard Genomic Region Type
replaced-gene-id	Replaced NCBI GeneID
rna-type	RNA Type
summary-sourcedate	Summary SourceDate
summary-sourcedescription	Summary SourceDescription
summary-sourcesource	Summary SourceSource
swissprot-accessions	SwissProt Accessions
symbol	Symbol
synonyms	Synonyms
tax-id	Taxonomic ID
tax-name	Taxonomic Name
transcript-count	Transcripts

Generated November 25, 2024