gene-product
Convert Gene Product Report into an Excel workbook
gene-product
Convert Gene Product Report into an Excel workbook
Name
dataformat excel gene-product - Convert Gene Product Report into an Excel workbook
Synopsis
dataformat excel gene-product [flags]
Description
Convert Gene Product Report into an Excel workbook.
Refer to NCBI’s download and install documentation for information about getting started with the command-line tools.
Examples
dataformat excel gene --inputfile gene_package/ncbi_dataset/data/product_report.jsonl --outputfile gene_products.xlsx
dataformat excel gene --package genes.zip --outputfile gene_products.xlsx
Options
--fields strings Comma-separated list of fields
--force Force dataformat to run without type check prompt
-h, --help help for gene-product
--inputfile string Input file (default "/dev/stdin")
--outputfile string Excel workbook file
--package string Data package (zip archive), inputfile parameter is relative to the root path inside the archive
Fields
| Mnemonic | Name |
|---|---|
| common-name | Common Name |
| description | Description |
| gene-id | NCBI GeneID |
| gene-type | Gene Type |
| protein-count | Protein Count |
| rna-type | RNA Type |
| symbol | Symbol |
| tax-id | Taxonomic ID |
| tax-name | Taxonomic Name |
| transcript-accession | Transcript Accession |
| transcript-cds-accession | Transcript CDS Sequence Accession |
| transcript-cds-range-order | Transcript CDS Order |
| transcript-cds-range-orientation | Transcript CDS Orientation |
| transcript-cds-range-start | Transcript CDS Start |
| transcript-cds-range-stop | Transcript CDS Stop |
| transcript-count | Transcript Count |
| transcript-ensembl-transcript | Transcript Ensembl Transcript |
| transcript-genomic-location-accession | Transcript Genomic Accession |
| transcript-genomic-location-exon-order | Transcript Genomic Exons Order |
| transcript-genomic-location-exon-orientation | Transcript Genomic Exons Orientation |
| transcript-genomic-location-exon-start | Transcript Genomic Exons Start |
| transcript-genomic-location-exon-stop | Transcript Genomic Exons Stop |
| transcript-genomic-location-range-order | Transcript Genomic Order |
| transcript-genomic-location-range-orientation | Transcript Genomic Orientation |
| transcript-genomic-location-range-start | Transcript Genomic Start |
| transcript-genomic-location-range-stop | Transcript Genomic Stop |
| transcript-genomic-location-seq-name | Transcript Genomic Seq Name |
| transcript-length | Transcript Transcript Length |
| transcript-name | Transcript Transcript Name |
| transcript-protein-accession | Transcript Protein Accession |
| transcript-protein-ensembl-protein | Transcript Protein Ensembl Protein |
| transcript-protein-isoform | Transcript Protein Isoform |
| transcript-protein-length | Transcript Protein Length |
| transcript-protein-mat-peptide-accession | Transcript Protein Mature Peptide Accession |
| transcript-protein-mat-peptide-length | Transcript Protein Mature Peptide Length |
| transcript-protein-mat-peptide-name | Transcript Protein Mature Peptide Name |
| transcript-protein-name | Transcript Protein Name |
| transcript-transcript-type | Transcript Type |