gene

Convert Gene Report into an Excel workbook

Contents

gene

Convert Gene Report into an Excel workbook

Name

dataformat excel gene - Convert Gene Report into an Excel workbook

Synopsis

dataformat excel gene [flags]

Description

Convert Gene Report into an Excel workbook.

Refer to NCBI’s command line start documentation for information about getting started with the command-line tools.

Examples

  dataformat excel gene --inputfile gene_package/ncbi_dataset/data/data_report.jsonl --outputfile genes.xlsx
  dataformat excel gene --package genes.zip --outputfile genes.xlsx

Options

      --fields strings      comma-separated list of fields
  -h, --help                help for gene
      --inputfile string    input file (default "/dev/stdin")
  -o, --outputfile string   Excel workbook file
      --package string      datasets package (zip archive), inputfile parameter is relative to the root path inside the archive

Fields

Mnemonic	Name
annotation-assemblies-in-scope-accession	Annotation Assemblies in Scope Accession
annotation-assemblies-in-scope-name	Annotation Assemblies in Scope 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-range-accession	Genomic Range Sequence Accession
genomic-range-range-order	Genomic Range Order
genomic-range-range-orientation	Genomic Range Orientation
genomic-range-range-start	Genomic Range Start
genomic-range-range-stop	Genomic Range Stop
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
name-authority	Nomenclature Authority
name-id	Nomenclature ID
omim-ids	OMIM IDs
orientation	Orientation
protein-accession	Protein Accession
protein-ensembl-protein	Protein Ensembl Protein
protein-isoform	Protein Isoform
protein-length	Protein Length
protein-mat-peptide-accession	Protein Mature Peptide Accession
protein-mat-peptide-length	Protein Mature Peptide Length
protein-mat-peptide-name	Protein Mature Peptide Name
protein-name	Protein Name
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
swissprot-accessions	SwissProt Accessions
symbol	Symbol
synonyms	Synonyms
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-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 November 25, 2024