gene

Convert Gene Report into an Excel workbook

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 download and install 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 field names that supports wildcards (*). Names with wildcards must be quoted, for example: annotation-assembly-accession,'*date','summary*'
      --force               Force dataformat to run without type check prompt
  -h, --help                help for gene
      --inputfile string    Input file (default "/dev/stdin")
      --outputfile string   Excel workbook file
      --package string      Data package (zip archive), inputfile parameter is relative to the root path inside the archive

Fields

MnemonicName
annotation-assembly-accessionAnnotation Assembly Accession
annotation-assembly-nameAnnotation Assembly Name
annotation-genomic-range-accessionAnnotation Genomic Range Accession
annotation-genomic-range-range-orderAnnotation Genomic Range Order
annotation-genomic-range-range-orientationAnnotation Genomic Range Orientation
annotation-genomic-range-range-startAnnotation Genomic Range Start
annotation-genomic-range-range-stopAnnotation Genomic Range Stop
annotation-genomic-range-seq-nameAnnotation Genomic Range Seq Name
annotation-release-dateAnnotation Release Date
annotation-release-nameAnnotation Release Name
chromosomesChromosomes
common-nameCommon Name
descriptionDescription
ensembl-geneidsEnsembl GeneIDs
gene-idNCBI GeneID
gene-typeGene Type
genomic-region-gene-range-accessionGenomic Region Gene Range Sequence Accession
genomic-region-gene-range-range-orderGenomic Region Gene Range Order
genomic-region-gene-range-range-orientationGenomic Region Gene Range Orientation
genomic-region-gene-range-range-startGenomic Region Gene Range Start
genomic-region-gene-range-range-stopGenomic Region Gene Range Stop
genomic-region-genomic-region-typeGenomic Region Genomic Region Type
go-assigned-byGene Ontology Assigned By
go-bp-evidence-codeGene Ontology Biological Process Evidence Code
go-bp-idGene Ontology Biological Process Go ID
go-bp-nameGene Ontology Biological Process Name
go-bp-qualifierGene Ontology Biological Process Qualifier
go-bp-reference-pmidGene Ontology Biological Process Reference PMID
go-cc-evidence-codeGene Ontology Cellular Component Evidence Code
go-cc-idGene Ontology Cellular Component Go ID
go-cc-nameGene Ontology Cellular Component Name
go-cc-qualifierGene Ontology Cellular Component Qualifier
go-cc-reference-pmidGene Ontology Cellular Component Reference PMID
go-mf-evidence-codeGene Ontology Molecular Function Evidence Code
go-mf-idGene Ontology Molecular Function Go ID
go-mf-nameGene Ontology Molecular Function Name
go-mf-qualifierGene Ontology Molecular Function Qualifier
go-mf-reference-pmidGene Ontology Molecular Function Reference PMID
group-idGene Group Identifier
group-methodGene Group Method
locus-tagLocus Tag
name-authorityNomenclature Authority
name-idNomenclature ID
omim-idsOMIM IDs
orientationOrientation
protein-countProteins
ref-standard-gene-range-accessionReference Standard Gene Range Sequence Accession
ref-standard-gene-range-range-orderReference Standard Gene Range Order
ref-standard-gene-range-range-orientationReference Standard Gene Range Orientation
ref-standard-gene-range-range-startReference Standard Gene Range Start
ref-standard-gene-range-range-stopReference Standard Gene Range Stop
ref-standard-genomic-region-typeReference Standard Genomic Region Type
replaced-gene-idReplaced NCBI GeneID
rna-typeRNA Type
summary-dateSummary Date
summary-descriptionSummary Description
summary-sourceSummary Source
swissprot-accessionsSwissProt Accessions
symbolSymbol
synonymsSynonyms
tax-idTaxonomic ID
tax-nameTaxonomic Name
transcript-countTranscripts
Generated February 26, 2025