ezgff_alpha

What is ezgff_alpha

Utilities for GFF3, the genome annotation format. Useful to explore the gene model features.

Pre-requisites

• sqlite3

Install

gem ezgff

Quick start

Build database from GFF3 file.

ezgff build in.gff3

Retrieve GFF3 reacod by ID.

ezgff view data.ezdb cds-WP_010895901.1 --with=ancestors

ezgff view data.ezdb cds-WP_010895901.1 --with=ancestors --format=json |jq

examples to use jq

ezgff_alpha/bin/ezgff view GCF_000009605.1_ASM960v1_genomic.gff.ezdb cds-WP_010895901.1  --with=ancestors --format=json  |jq -r '.gff_records | map(select(.type == "gene"))[0] | [.seqid, .start, .end, .attributes.gene] |@csv'