virus-annotation

Convert Virus Annotation Report into TSV format

Contents

virus-annotation

Convert Virus Annotation Report into TSV format

Name

dataformat tsv virus-annotation - Convert Virus Annotation Report into TSV format

Synopsis

dataformat tsv virus-annotation [flags]

Description

Convert Virus Annotation 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 virus-annotation --inputfile sars2_package/ncbi_dataset/data/annotation_report.jsonl
  dataformat tsv virus-annotation --package virus-sars2-refseq.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 virus-annotation
      --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
accession	Accession
gene-cds-accession	Gene CDS Accession
gene-cds-cdd-accession	Gene CDS CDD Accession
gene-cds-cdd-name	Gene CDS CDD Name
gene-cds-cdd-range-order	Gene CDS CDD Range Order
gene-cds-cdd-range-orientation	Gene CDS CDD Range Orientation
gene-cds-cdd-range-start	Gene CDS CDD Range Start
gene-cds-cdd-range-stop	Gene CDS CDD Range Stop
gene-cds-mat-peptide-accession	Gene CDS Mature Peptide Accession
gene-cds-mat-peptide-cdd-accession	Gene CDS Mature Peptide CDD Accession
gene-cds-mat-peptide-cdd-name	Gene CDS Mature Peptide CDD Name
gene-cds-mat-peptide-cdd-range-order	Gene CDS Mature Peptide CDD Range Order
gene-cds-mat-peptide-cdd-range-orientation	Gene CDS Mature Peptide CDD Range Orientation
gene-cds-mat-peptide-cdd-range-start	Gene CDS Mature Peptide CDD Range Start
gene-cds-mat-peptide-cdd-range-stop	Gene CDS Mature Peptide CDD Range Stop
gene-cds-mat-peptide-name	Gene CDS Mature Peptide Name
gene-cds-mat-peptide-nuc-fasta-accession	Gene CDS Mature Peptide Nucleotide FASTA Accession
gene-cds-mat-peptide-nuc-fasta-hash	Gene CDS Mature Peptide Nucleotide FASTA Hash
gene-cds-mat-peptide-nuc-fasta-range-order	Gene CDS Mature Peptide Nucleotide FASTA Range Order
gene-cds-mat-peptide-nuc-fasta-range-orientation	Gene CDS Mature Peptide Nucleotide FASTA Range Orientation
gene-cds-mat-peptide-nuc-fasta-range-start	Gene CDS Mature Peptide Nucleotide FASTA Range Start
gene-cds-mat-peptide-nuc-fasta-range-stop	Gene CDS Mature Peptide Nucleotide FASTA Range Stop
gene-cds-mat-peptide-nuc-fasta-seq-id	Gene CDS Mature Peptide Nucleotide FASTA Sequence ID
gene-cds-mat-peptide-nuc-fasta-title	Gene CDS Mature Peptide Nucleotide FASTA Title
gene-cds-mat-peptide-other-names	Gene CDS Mature Peptide Other Names
gene-cds-mat-peptide-pdb-ids	Gene CDS Mature Peptide PDB IDs
gene-cds-mat-peptide-prot-completeness	Gene CDS Mature Peptide Protein Completeness
gene-cds-mat-peptide-protein-fasta-accession	Gene CDS Mature Peptide Protein FASTA Accession
gene-cds-mat-peptide-protein-fasta-hash	Gene CDS Mature Peptide Protein FASTA Hash
gene-cds-mat-peptide-protein-fasta-range-order	Gene CDS Mature Peptide Protein FASTA Range Order
gene-cds-mat-peptide-protein-fasta-range-orientation	Gene CDS Mature Peptide Protein FASTA Range Orientation
gene-cds-mat-peptide-protein-fasta-range-start	Gene CDS Mature Peptide Protein FASTA Range Start
gene-cds-mat-peptide-protein-fasta-range-stop	Gene CDS Mature Peptide Protein FASTA Range Stop
gene-cds-mat-peptide-protein-fasta-seq-id	Gene CDS Mature Peptide Protein FASTA Sequence ID
gene-cds-mat-peptide-protein-fasta-title	Gene CDS Mature Peptide Protein FASTA Title
gene-cds-mat-peptide-uniprot-id	Gene CDS Mature Peptide UniProtID
gene-cds-mat-peptide-uniprot-name	Gene CDS Mature Peptide UniProtName
gene-cds-name	Gene CDS Name
gene-cds-nuc-fasta-accession	Gene CDS Nucleotide FASTA Accession
gene-cds-nuc-fasta-hash	Gene CDS Nucleotide FASTA Hash
gene-cds-nuc-fasta-range-order	Gene CDS Nucleotide FASTA Range Order
gene-cds-nuc-fasta-range-orientation	Gene CDS Nucleotide FASTA Range Orientation
gene-cds-nuc-fasta-range-start	Gene CDS Nucleotide FASTA Range Start
gene-cds-nuc-fasta-range-stop	Gene CDS Nucleotide FASTA Range Stop
gene-cds-nuc-fasta-seq-id	Gene CDS Nucleotide FASTA Sequence ID
gene-cds-nuc-fasta-title	Gene CDS Nucleotide FASTA Title
gene-cds-other-names	Gene CDS Other Names
gene-cds-pdb-ids	Gene CDS PDB IDs
gene-cds-prot-completeness	Gene CDS Protein Completeness
gene-cds-protein-fasta-accession	Gene CDS Protein FASTA Accession
gene-cds-protein-fasta-hash	Gene CDS Protein FASTA Hash
gene-cds-protein-fasta-range-order	Gene CDS Protein FASTA Range Order
gene-cds-protein-fasta-range-orientation	Gene CDS Protein FASTA Range Orientation
gene-cds-protein-fasta-range-start	Gene CDS Protein FASTA Range Start
gene-cds-protein-fasta-range-stop	Gene CDS Protein FASTA Range Stop
gene-cds-protein-fasta-seq-id	Gene CDS Protein FASTA Sequence ID
gene-cds-protein-fasta-title	Gene CDS Protein FASTA Title
gene-cds-uniprot-id	Gene CDS UniProtID
gene-cds-uniprot-name	Gene CDS UniProtName
gene-gene-id	Gene NCBI GeneID
gene-genomic-accession	Gene Genomic Accession
gene-genomic-hash	Gene Genomic Hash
gene-genomic-range-order	Gene Genomic Range Order
gene-genomic-range-orientation	Gene Genomic Range Orientation
gene-genomic-range-start	Gene Genomic Range Start
gene-genomic-range-stop	Gene Genomic Range Stop
gene-genomic-seq-id	Gene Genomic Sequence ID
gene-genomic-title	Gene Genomic Title
gene-name	Gene Name
isolate-name	Isolate name

Generated April 19, 2024