prok-gene-location
Convert Prokaryote Gene Location Report into an Excel workbook
prok-gene-location
Convert Prokaryote Gene Location Report into an Excel workbook
Name
dataformat excel prok-gene-location - Convert Prokaryote Gene Location Report into an Excel workbook
Synopsis
dataformat excel prok-gene-location [flags]
Description
Convert Prokaryote Gene Location Report into an Excel workbook.
Refer to NCBI’s command line start documentation for information about getting started with the command-line tools.
Examples
dataformat excel prok-gene-location --inputfile prokaryote_package/ncbi_dataset/data/annotation_report.jsonl --outputfile prokaryote.xlsx
dataformat excel prok-gene-location --package prokaryote-package.zip --outputfile prokaryote.xlsx
Options
--fields strings comma-separated list of fields
-h, --help help for prok-gene-location
--inputfile string input file (default "/dev/stdin")
-o, --outputfile string Excel workbook file
--package string datasets package (zip archive), inputfile parameter is relative to the root path inside the archive
Fields
| Mnemonic | Name |
|---|---|
| chromosome_name | Chromosome |
| completeness | Completeness |
| genbank-genomic-location-assembly-accession | GenBank Genomic Location Assembly Accession |
| genbank-genomic-location-seq-range-accession | GenBank Genomic Location Sequence Accession |
| genbank-genomic-location-seq-range-range-order | GenBank Genomic Location Order |
| genbank-genomic-location-seq-range-range-orientation | GenBank Genomic Location Orientation |
| genbank-genomic-location-seq-range-range-start | GenBank Genomic Location Start |
| genbank-genomic-location-seq-range-range-stop | GenBank Genomic Location Stop |
| organism-common-name | Organism Common Name |
| organism-organism-name | Organism Organism Name |
| organism-pangolin | Organism Pangolin Classification |
| organism-strain | Organism Strain |
| organism-tax-id | Organism Taxonomic ID |
| protein-accession | Protein Accession |
| refseq-genomic-location-assembly-accession | RefSeq Genomic Location Assembly Accession |
| refseq-genomic-location-seq-range-accession | RefSeq Genomic Location Sequence Accession |
| refseq-genomic-location-seq-range-range-order | RefSeq Genomic Location Order |
| refseq-genomic-location-seq-range-range-orientation | RefSeq Genomic Location Orientation |
| refseq-genomic-location-seq-range-range-start | RefSeq Genomic Location Start |
| refseq-genomic-location-seq-range-range-stop | RefSeq Genomic Location Stop |