genome-annotations
Convert Genome Annotation Report into TSV format
genome-annotations
Convert Genome Annotation Report into TSV format
Name
dataformat tsv genome-annotations - Convert Genome Annotation Report into TSV format
Synopsis
dataformat tsv genome-annotations [flags]
Description
Convert Genome 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 genome-annotations --inputfile annotation_report.jsonl
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 genome-annotations
--inputfile string Input file (default "/dev/stdin")
--list-templates List all all available templates for this report type
--package string Data package (zip archive), inputfile parameter is relative to the root path inside the archive
--template string Pre-defined output format for the current report type
Fields
| Mnemonic | Name |
|---|---|
| annotation-assembly-accession | Annotation Assembly Accession |
| annotation-assembly-name | Annotation Assembly Name |
| annotation-genomic-range-accession | Annotation Genomic Range Accession |
| annotation-genomic-range-exon-order | Annotation Genomic Range Exons Order |
| annotation-genomic-range-exon-orientation | Annotation Genomic Range Exons Orientation |
| annotation-genomic-range-exon-start | Annotation Genomic Range Exons Start |
| annotation-genomic-range-exon-stop | Annotation Genomic Range Exons Stop |
| annotation-genomic-range-range-order | Annotation Genomic Range Order |
| annotation-genomic-range-range-orientation | Annotation Genomic Range Orientation |
| annotation-genomic-range-range-start | Annotation Genomic Range Start |
| annotation-genomic-range-range-stop | Annotation Genomic Range Stop |
| annotation-genomic-range-seq-name | Annotation Genomic Range Seq Name |
| annotation-release-date | Annotation Release Date |
| annotation-release-name | Annotation Release Name |
| chromosomes | Chromosomes |
| common-name | Common Name |
| ensembl-geneids | Ensembl GeneIDs |
| gene-id | NCBI GeneID |
| gene-type | Gene Type |
| genomic-region-gene-range-accession | Genomic Region Gene Range Sequence Accession |
| genomic-region-gene-range-range-order | Genomic Region Gene Range Order |
| genomic-region-gene-range-range-orientation | Genomic Region Gene Range Orientation |
| genomic-region-gene-range-range-start | Genomic Region Gene Range Start |
| genomic-region-gene-range-range-stop | Genomic Region Gene Range Stop |
| genomic-region-genomic-region-type | Genomic Region Genomic Region Type |
| locus-tag | Locus Tag |
| name | Name |
| omim-ids | OMIM IDs |
| orientation | Orientation |
| ref-standard-gene-range-accession | Reference Standard Gene Range Sequence Accession |
| ref-standard-gene-range-range-order | Reference Standard Gene Range Order |
| ref-standard-gene-range-range-orientation | Reference Standard Gene Range Orientation |
| ref-standard-gene-range-range-start | Reference Standard Gene Range Start |
| ref-standard-gene-range-range-stop | Reference Standard Gene Range Stop |
| ref-standard-genomic-region-type | Reference Standard Genomic Region Type |
| rna-type | RNA Type |
| swissprot-accessions | SwissProt Accessions |
| symbol | Symbol |
| synonyms | Synonyms |
| tax-id | Taxonomic ID |
| tax-name | Taxonomic Name |