GFF_DIFF

A tool to generate a diff (in JSON format) between two GFF3 files, written in Rust.

Install rust

See instructions, or just run:

curl https://sh.rustup.rs -sSf | sh

Compile the tool

Use git clone https://github.com/magnusmanske/gff_diff.git to get the tool source, then use

cargo build --release

to build the binary (target/release/gff_diff).

Usage

To compare original.gff and modified.gff, use:

gff_diff original.gff modified.gff

Output format

Output is a JSON structure. The changes required to turn original.gff into modified.gff are in the objects in the {"changes":[]} array. Each object has an action, a what, and an id key. what can be row (a line in the GFF file, represented by an id) or attribute (last column in a row).

action can be:

• add / remove for what=attribute
• add / remove / update for what=row

For what=row / action=update, there are key and value keys, indicating what should be changed. key can be one of seqname, source, feature_type, start , end, score, strand, or frame. value is a string representing the new value for the given key.

For what=row / action=add/remove, a data key holds a JSON structure representing the entire row to be added or removed.

For what=attribute / action=add/remove, there are key and value keys, indicating what value should be added to, or removed from, the attribute key.