Annotate Module

The annotate module provides functions for functionally annotating predicted genes.

Key Functions

annotate

This is the main function for functionally annotating predicted genes. It takes a GFF3 file with gene predictions as input and produces various annotation files as output.

check_inputs

Checks that the input files exist and are valid.

find_input_files

Finds input files in the specified directory.

parse_annotations

Parses annotation results from various sources and adds them to the gene models.

naming_slug

Generates a slug for the species and strain combination.

_sortDict

Sorts a dictionary by location.