virus-genome

Convert Virus Data Report into TSV format

virus-genome

Convert Virus Data Report into TSV format

Name

dataformat tsv virus-genome - Convert Virus Data Report into TSV format

Synopsis

dataformat tsv virus-genome [flags]

Description

Convert Virus Data 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 virus-genome --inputfile sars2_package/ncbi_dataset/data/data_report.jsonl
  dataformat tsv virus-genome --package virus-sars2-refseq.zip

Options

      --elide-header       Do not output header
      --fields strings     comma-separated list of fields
  -h, --help               help for virus-genome
      --inputfile string   input file (default "/dev/stdin")
      --package string     datasets package (zip archive), inputfile parameter is relative to the root path inside the archive

Fields

MnemonicName
accessionAccession
annot-gene-cds-accessionAnnotation Gene CDS Accession
annot-gene-cds-cdd-accessionAnnotation Gene CDS CDD Accession
annot-gene-cds-cdd-nameAnnotation Gene CDS CDD Name
annot-gene-cds-cdd-range-orderAnnotation Gene CDS CDD Range Order
annot-gene-cds-cdd-range-orientationAnnotation Gene CDS CDD Range Orientation
annot-gene-cds-cdd-range-startAnnotation Gene CDS CDD Range Start
annot-gene-cds-cdd-range-stopAnnotation Gene CDS CDD Range Stop
annot-gene-cds-mat-peptide-accessionAnnotation Gene CDS Mature Peptide Accession
annot-gene-cds-mat-peptide-cdd-accessionAnnotation Gene CDS Mature Peptide CDD Accession
annot-gene-cds-mat-peptide-cdd-nameAnnotation Gene CDS Mature Peptide CDD Name
annot-gene-cds-mat-peptide-cdd-range-orderAnnotation Gene CDS Mature Peptide CDD Range Order
annot-gene-cds-mat-peptide-cdd-range-orientationAnnotation Gene CDS Mature Peptide CDD Range Orientation
annot-gene-cds-mat-peptide-cdd-range-startAnnotation Gene CDS Mature Peptide CDD Range Start
annot-gene-cds-mat-peptide-cdd-range-stopAnnotation Gene CDS Mature Peptide CDD Range Stop
annot-gene-cds-mat-peptide-nameAnnotation Gene CDS Mature Peptide Name
annot-gene-cds-mat-peptide-nuc-fasta-accessionAnnotation Gene CDS Mature Peptide Nucleotide FASTA Accession
annot-gene-cds-mat-peptide-nuc-fasta-hashAnnotation Gene CDS Mature Peptide Nucleotide FASTA Hash
annot-gene-cds-mat-peptide-nuc-fasta-range-orderAnnotation Gene CDS Mature Peptide Nucleotide FASTA Range Order
annot-gene-cds-mat-peptide-nuc-fasta-range-orientationAnnotation Gene CDS Mature Peptide Nucleotide FASTA Range Orientation
annot-gene-cds-mat-peptide-nuc-fasta-range-startAnnotation Gene CDS Mature Peptide Nucleotide FASTA Range Start
annot-gene-cds-mat-peptide-nuc-fasta-range-stopAnnotation Gene CDS Mature Peptide Nucleotide FASTA Range Stop
annot-gene-cds-mat-peptide-nuc-fasta-seq-idAnnotation Gene CDS Mature Peptide Nucleotide FASTA Sequence ID
annot-gene-cds-mat-peptide-nuc-fasta-titleAnnotation Gene CDS Mature Peptide Nucleotide FASTA Title
annot-gene-cds-mat-peptide-other-namesAnnotation Gene CDS Mature Peptide Other Names
annot-gene-cds-mat-peptide-pdb-idsAnnotation Gene CDS Mature Peptide PDB IDs
annot-gene-cds-mat-peptide-prot-completenessAnnotation Gene CDS Mature Peptide Protein Completeness
annot-gene-cds-mat-peptide-protein-fasta-accessionAnnotation Gene CDS Mature Peptide Protein FASTA Accession
annot-gene-cds-mat-peptide-protein-fasta-hashAnnotation Gene CDS Mature Peptide Protein FASTA Hash
annot-gene-cds-mat-peptide-protein-fasta-range-orderAnnotation Gene CDS Mature Peptide Protein FASTA Range Order
annot-gene-cds-mat-peptide-protein-fasta-range-orientationAnnotation Gene CDS Mature Peptide Protein FASTA Range Orientation
annot-gene-cds-mat-peptide-protein-fasta-range-startAnnotation Gene CDS Mature Peptide Protein FASTA Range Start
annot-gene-cds-mat-peptide-protein-fasta-range-stopAnnotation Gene CDS Mature Peptide Protein FASTA Range Stop
annot-gene-cds-mat-peptide-protein-fasta-seq-idAnnotation Gene CDS Mature Peptide Protein FASTA Sequence ID
annot-gene-cds-mat-peptide-protein-fasta-titleAnnotation Gene CDS Mature Peptide Protein FASTA Title
annot-gene-cds-mat-peptide-uniprot-idAnnotation Gene CDS Mature Peptide UniProtID
annot-gene-cds-mat-peptide-uniprot-nameAnnotation Gene CDS Mature Peptide UniProtName
annot-gene-cds-nameAnnotation Gene CDS Name
annot-gene-cds-nuc-fasta-accessionAnnotation Gene CDS Nucleotide FASTA Accession
annot-gene-cds-nuc-fasta-hashAnnotation Gene CDS Nucleotide FASTA Hash
annot-gene-cds-nuc-fasta-range-orderAnnotation Gene CDS Nucleotide FASTA Range Order
annot-gene-cds-nuc-fasta-range-orientationAnnotation Gene CDS Nucleotide FASTA Range Orientation
annot-gene-cds-nuc-fasta-range-startAnnotation Gene CDS Nucleotide FASTA Range Start
annot-gene-cds-nuc-fasta-range-stopAnnotation Gene CDS Nucleotide FASTA Range Stop
annot-gene-cds-nuc-fasta-seq-idAnnotation Gene CDS Nucleotide FASTA Sequence ID
annot-gene-cds-nuc-fasta-titleAnnotation Gene CDS Nucleotide FASTA Title
annot-gene-cds-other-namesAnnotation Gene CDS Other Names
annot-gene-cds-pdb-idsAnnotation Gene CDS PDB IDs
annot-gene-cds-prot-completenessAnnotation Gene CDS Protein Completeness
annot-gene-cds-protein-fasta-accessionAnnotation Gene CDS Protein FASTA Accession
annot-gene-cds-protein-fasta-hashAnnotation Gene CDS Protein FASTA Hash
annot-gene-cds-protein-fasta-range-orderAnnotation Gene CDS Protein FASTA Range Order
annot-gene-cds-protein-fasta-range-orientationAnnotation Gene CDS Protein FASTA Range Orientation
annot-gene-cds-protein-fasta-range-startAnnotation Gene CDS Protein FASTA Range Start
annot-gene-cds-protein-fasta-range-stopAnnotation Gene CDS Protein FASTA Range Stop
annot-gene-cds-protein-fasta-seq-idAnnotation Gene CDS Protein FASTA Sequence ID
annot-gene-cds-protein-fasta-titleAnnotation Gene CDS Protein FASTA Title
annot-gene-cds-uniprot-idAnnotation Gene CDS UniProtID
annot-gene-cds-uniprot-nameAnnotation Gene CDS UniProtName
annot-gene-gene-idAnnotation Gene NCBI GeneID
annot-gene-genomic-accessionAnnotation Gene Genomic Accession
annot-gene-genomic-hashAnnotation Gene Genomic Hash
annot-gene-genomic-range-orderAnnotation Gene Genomic Range Order
annot-gene-genomic-range-orientationAnnotation Gene Genomic Range Orientation
annot-gene-genomic-range-startAnnotation Gene Genomic Range Start
annot-gene-genomic-range-stopAnnotation Gene Genomic Range Stop
annot-gene-genomic-seq-idAnnotation Gene Genomic Sequence ID
annot-gene-genomic-titleAnnotation Gene Genomic Title
annot-gene-nameAnnotation Gene Name
bioprojectsBioProjects
biosample-accBioSample accession
completenessCompleteness
gene-countGene count
geo-locationGeographic location
geo-regionGeographic region
host-common-nameHost Common Name
host-organism-nameHost Organism Name
host-pangolinHost Pangolin Classification
host-strainHost Strain
host-tax-idHost Taxonomic ID
is-annotatedIs Annotated
is-completeIs Complete
isolate-collection-dateIsolate Collection date
isolate-lineageIsolate Lineage
isolate-lineage-sourceIsolate Lineage source
lengthLength
matpeptide-countMature peptide count
mol-typeMolecule type
nucleotide-completenessNucleotide completeness
protein-countProtein count
purpose-of-samplingPurpose of Sampling
release-dateRelease date
sourcedbSource database
sra-accsSRA Accessions
update-dateUpdate date
virus-common-nameVirus Common Name
virus-organism-nameVirus Organism Name
virus-pangolinVirus Pangolin Classification
virus-strainVirus Strain
virus-tax-idVirus Taxonomic ID
Generated October 5, 2022