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
Mnemonic | Name |
---|---|
accession | Accession |
annot-gene-cds-accession | Annotation Gene CDS Accession |
annot-gene-cds-cdd-accession | Annotation Gene CDS CDD Accession |
annot-gene-cds-cdd-name | Annotation Gene CDS CDD Name |
annot-gene-cds-cdd-range-order | Annotation Gene CDS CDD Range Order |
annot-gene-cds-cdd-range-orientation | Annotation Gene CDS CDD Range Orientation |
annot-gene-cds-cdd-range-start | Annotation Gene CDS CDD Range Start |
annot-gene-cds-cdd-range-stop | Annotation Gene CDS CDD Range Stop |
annot-gene-cds-mat-peptide-accession | Annotation Gene CDS Mature Peptide Accession |
annot-gene-cds-mat-peptide-cdd-accession | Annotation Gene CDS Mature Peptide CDD Accession |
annot-gene-cds-mat-peptide-cdd-name | Annotation Gene CDS Mature Peptide CDD Name |
annot-gene-cds-mat-peptide-cdd-range-order | Annotation Gene CDS Mature Peptide CDD Range Order |
annot-gene-cds-mat-peptide-cdd-range-orientation | Annotation Gene CDS Mature Peptide CDD Range Orientation |
annot-gene-cds-mat-peptide-cdd-range-start | Annotation Gene CDS Mature Peptide CDD Range Start |
annot-gene-cds-mat-peptide-cdd-range-stop | Annotation Gene CDS Mature Peptide CDD Range Stop |
annot-gene-cds-mat-peptide-name | Annotation Gene CDS Mature Peptide Name |
annot-gene-cds-mat-peptide-nuc-fasta-accession | Annotation Gene CDS Mature Peptide Nucleotide FASTA Accession |
annot-gene-cds-mat-peptide-nuc-fasta-hash | Annotation Gene CDS Mature Peptide Nucleotide FASTA Hash |
annot-gene-cds-mat-peptide-nuc-fasta-range-order | Annotation Gene CDS Mature Peptide Nucleotide FASTA Range Order |
annot-gene-cds-mat-peptide-nuc-fasta-range-orientation | Annotation Gene CDS Mature Peptide Nucleotide FASTA Range Orientation |
annot-gene-cds-mat-peptide-nuc-fasta-range-start | Annotation Gene CDS Mature Peptide Nucleotide FASTA Range Start |
annot-gene-cds-mat-peptide-nuc-fasta-range-stop | Annotation Gene CDS Mature Peptide Nucleotide FASTA Range Stop |
annot-gene-cds-mat-peptide-nuc-fasta-seq-id | Annotation Gene CDS Mature Peptide Nucleotide FASTA Sequence ID |
annot-gene-cds-mat-peptide-nuc-fasta-title | Annotation Gene CDS Mature Peptide Nucleotide FASTA Title |
annot-gene-cds-mat-peptide-other-names | Annotation Gene CDS Mature Peptide Other Names |
annot-gene-cds-mat-peptide-pdb-ids | Annotation Gene CDS Mature Peptide PDB IDs |
annot-gene-cds-mat-peptide-prot-completeness | Annotation Gene CDS Mature Peptide Protein Completeness |
annot-gene-cds-mat-peptide-protein-fasta-accession | Annotation Gene CDS Mature Peptide Protein FASTA Accession |
annot-gene-cds-mat-peptide-protein-fasta-hash | Annotation Gene CDS Mature Peptide Protein FASTA Hash |
annot-gene-cds-mat-peptide-protein-fasta-range-order | Annotation Gene CDS Mature Peptide Protein FASTA Range Order |
annot-gene-cds-mat-peptide-protein-fasta-range-orientation | Annotation Gene CDS Mature Peptide Protein FASTA Range Orientation |
annot-gene-cds-mat-peptide-protein-fasta-range-start | Annotation Gene CDS Mature Peptide Protein FASTA Range Start |
annot-gene-cds-mat-peptide-protein-fasta-range-stop | Annotation Gene CDS Mature Peptide Protein FASTA Range Stop |
annot-gene-cds-mat-peptide-protein-fasta-seq-id | Annotation Gene CDS Mature Peptide Protein FASTA Sequence ID |
annot-gene-cds-mat-peptide-protein-fasta-title | Annotation Gene CDS Mature Peptide Protein FASTA Title |
annot-gene-cds-mat-peptide-uniprot-id | Annotation Gene CDS Mature Peptide UniProtID |
annot-gene-cds-mat-peptide-uniprot-name | Annotation Gene CDS Mature Peptide UniProtName |
annot-gene-cds-name | Annotation Gene CDS Name |
annot-gene-cds-nuc-fasta-accession | Annotation Gene CDS Nucleotide FASTA Accession |
annot-gene-cds-nuc-fasta-hash | Annotation Gene CDS Nucleotide FASTA Hash |
annot-gene-cds-nuc-fasta-range-order | Annotation Gene CDS Nucleotide FASTA Range Order |
annot-gene-cds-nuc-fasta-range-orientation | Annotation Gene CDS Nucleotide FASTA Range Orientation |
annot-gene-cds-nuc-fasta-range-start | Annotation Gene CDS Nucleotide FASTA Range Start |
annot-gene-cds-nuc-fasta-range-stop | Annotation Gene CDS Nucleotide FASTA Range Stop |
annot-gene-cds-nuc-fasta-seq-id | Annotation Gene CDS Nucleotide FASTA Sequence ID |
annot-gene-cds-nuc-fasta-title | Annotation Gene CDS Nucleotide FASTA Title |
annot-gene-cds-other-names | Annotation Gene CDS Other Names |
annot-gene-cds-pdb-ids | Annotation Gene CDS PDB IDs |
annot-gene-cds-prot-completeness | Annotation Gene CDS Protein Completeness |
annot-gene-cds-protein-fasta-accession | Annotation Gene CDS Protein FASTA Accession |
annot-gene-cds-protein-fasta-hash | Annotation Gene CDS Protein FASTA Hash |
annot-gene-cds-protein-fasta-range-order | Annotation Gene CDS Protein FASTA Range Order |
annot-gene-cds-protein-fasta-range-orientation | Annotation Gene CDS Protein FASTA Range Orientation |
annot-gene-cds-protein-fasta-range-start | Annotation Gene CDS Protein FASTA Range Start |
annot-gene-cds-protein-fasta-range-stop | Annotation Gene CDS Protein FASTA Range Stop |
annot-gene-cds-protein-fasta-seq-id | Annotation Gene CDS Protein FASTA Sequence ID |
annot-gene-cds-protein-fasta-title | Annotation Gene CDS Protein FASTA Title |
annot-gene-cds-uniprot-id | Annotation Gene CDS UniProtID |
annot-gene-cds-uniprot-name | Annotation Gene CDS UniProtName |
annot-gene-gene-id | Annotation Gene NCBI GeneID |
annot-gene-genomic-accession | Annotation Gene Genomic Accession |
annot-gene-genomic-hash | Annotation Gene Genomic Hash |
annot-gene-genomic-range-order | Annotation Gene Genomic Range Order |
annot-gene-genomic-range-orientation | Annotation Gene Genomic Range Orientation |
annot-gene-genomic-range-start | Annotation Gene Genomic Range Start |
annot-gene-genomic-range-stop | Annotation Gene Genomic Range Stop |
annot-gene-genomic-seq-id | Annotation Gene Genomic Sequence ID |
annot-gene-genomic-title | Annotation Gene Genomic Title |
annot-gene-name | Annotation Gene Name |
bioprojects | BioProjects |
biosample-acc | BioSample accession |
completeness | Completeness |
gene-count | Gene count |
geo-location | Geographic location |
geo-region | Geographic region |
host-common-name | Host Common Name |
host-organism-name | Host Organism Name |
host-pangolin | Host Pangolin Classification |
host-strain | Host Strain |
host-tax-id | Host Taxonomic ID |
is-annotated | Is Annotated |
is-complete | Is Complete |
isolate-collection-date | Isolate Collection date |
isolate-lineage | Isolate Lineage |
isolate-lineage-source | Isolate Lineage source |
length | Length |
matpeptide-count | Mature peptide count |
mol-type | Molecule type |
nucleotide-completeness | Nucleotide completeness |
protein-count | Protein count |
purpose-of-sampling | Purpose of Sampling |
release-date | Release date |
sourcedb | Source database |
sra-accs | SRA Accessions |
update-date | Update date |
virus-common-name | Virus Common Name |
virus-organism-name | Virus Organism Name |
virus-pangolin | Virus Pangolin Classification |
virus-strain | Virus Strain |
virus-tax-id | Virus Taxonomic ID |