gene

Convert Gene Report into TSV format

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 command line start 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
  -h, --help               help for gene
      --inputfile string   input file
      --package string     datasets package (zip archive), inputfile parameter is relative to the root path inside the archive

Fields

MnemonicName
annotation-assemblies-in-scope-accessionAnnotation Assemblies in Scope Accession
annotation-assemblies-in-scope-nameAnnotation Assemblies in Scope 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-range-accessionGenomic Range Sequence Accession
genomic-range-range-orientationGenomic Range Orientation
genomic-range-range-startGenomic Range Start
genomic-range-range-stopGenomic Range Stop
genomic-region-gene-range-accessionGenomic Region Gene Range Sequence Accession
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
name-authorityNomenclature Authority
name-idNomenclature ID
omim-idsOMIM IDs
orientationOrientation
protein-accessionProtein Accession
protein-ensembl-proteinProtein Ensembl Protein
protein-isoformProtein Isoform
protein-lengthProtein Length
protein-mat-peptide-accessionProtein Mature Peptide Accession
protein-mat-peptide-lengthProtein Mature Peptide Length
protein-mat-peptide-nameProtein Mature Peptide Name
protein-nameProtein Name
ref-standard-gene-range-accessionReference Standard Gene Range Sequence Accession
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
swissprot-accessionsSwissProt Accessions
symbolSymbol
synonymsSynonyms
tax-idTaxonomic ID
tax-nameTaxonomic Name
transcript-accessionTranscript Accession
transcript-cds-accessionTranscript CDS Sequence Accession
transcript-cds-range-orientationTranscript CDS Orientation
transcript-cds-range-startTranscript CDS Start
transcript-cds-range-stopTranscript CDS Stop
transcript-ensembl-transcriptTranscript Ensembl Transcript
transcript-genomic-location-accessionTranscript Genomic Accession
transcript-genomic-location-exon-orientationTranscript Genomic Exons Orientation
transcript-genomic-location-exon-startTranscript Genomic Exons Start
transcript-genomic-location-exon-stopTranscript Genomic Exons Stop
transcript-genomic-location-range-orientationTranscript Genomic Orientation
transcript-genomic-location-range-startTranscript Genomic Start
transcript-genomic-location-range-stopTranscript Genomic Stop
transcript-genomic-location-seq-nameTranscript Genomic Seq Name
transcript-lengthTranscript Transcript Length
transcript-nameTranscript Transcript Name
transcript-protein-accessionTranscript Protein Accession
transcript-protein-ensembl-proteinTranscript Protein Ensembl Protein
transcript-protein-isoformTranscript Protein Isoform
transcript-protein-lengthTranscript Protein Length
transcript-protein-mat-peptide-accessionTranscript Protein Mature Peptide Accession
transcript-protein-mat-peptide-lengthTranscript Protein Mature Peptide Length
transcript-protein-mat-peptide-nameTranscript Protein Mature Peptide Name
transcript-protein-nameTranscript Protein Name
transcript-transcript-typeTranscript Type
Generated November 19, 2021