gene-product

Convert Gene Product Report into TSV format

Contents

gene-product

Convert Gene Product Report into TSV format

Name

dataformat tsv gene-product - Convert Gene Product Report into TSV format

Synopsis

dataformat tsv gene-product [flags]

Description

Convert Gene Product 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/product_report.jsonl
  dataformat tsv gene --package gene_products.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-product
      --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
common-name	Common Name
description	Description
gene-id	NCBI GeneID
gene-type	Gene Type
protein-count	Protein Count
rna-type	RNA Type
symbol	Symbol
tax-id	Taxonomic ID
tax-name	Taxonomic Name
transcript-accession	Transcript Accession
transcript-cds-accession	Transcript CDS Sequence Accession
transcript-cds-range-order	Transcript CDS Order
transcript-cds-range-orientation	Transcript CDS Orientation
transcript-cds-range-start	Transcript CDS Start
transcript-cds-range-stop	Transcript CDS Stop
transcript-count	Transcript Count
transcript-ensembl-transcript	Transcript Ensembl Transcript
transcript-genomic-location-accession	Transcript Genomic Accession
transcript-genomic-location-exon-order	Transcript Genomic Exons Order
transcript-genomic-location-exon-orientation	Transcript Genomic Exons Orientation
transcript-genomic-location-exon-start	Transcript Genomic Exons Start
transcript-genomic-location-exon-stop	Transcript Genomic Exons Stop
transcript-genomic-location-range-order	Transcript Genomic Order
transcript-genomic-location-range-orientation	Transcript Genomic Orientation
transcript-genomic-location-range-start	Transcript Genomic Start
transcript-genomic-location-range-stop	Transcript Genomic Stop
transcript-genomic-location-seq-name	Transcript Genomic Seq Name
transcript-length	Transcript Transcript Length
transcript-name	Transcript Transcript Name
transcript-protein-accession	Transcript Protein Accession
transcript-protein-ensembl-protein	Transcript Protein Ensembl Protein
transcript-protein-isoform	Transcript Protein Isoform
transcript-protein-length	Transcript Protein Length
transcript-protein-mat-peptide-accession	Transcript Protein Mature Peptide Accession
transcript-protein-mat-peptide-length	Transcript Protein Mature Peptide Length
transcript-protein-mat-peptide-name	Transcript Protein Mature Peptide Name
transcript-protein-name	Transcript Protein Name
transcript-transcript-type	Transcript Type

Generated April 16, 2024