OrthoFinder Tools

Idea

• Calculate the most common gene name of each orthogroup by majority vote: annotate_orthogroups
• Create plots analogous to roary_plots: orthofinder_plots

Setup

pip install orthofinder-tools

Usage

annotate_orthogroups

Prerequisites

Your FASTA sequences must have some description, e.g.:

>gnl|extdb|STRAIN-XY_000001 DNA-directed RNA polymerase subunit beta' [Pediococcus stilesii]
MIDVNKFESMQIGLASPDKIRMWSYGEVKKPETINYRTLKPEKDGLFDERIFGPTKDYECACGKYKRIRY
...

From this protein, DNA-directed RNA polymerase subunit beta' will be extracted.

Command line usage

annotate_orthogroups --help

annotate_orthogroups \
    --orthogroups_tsv /path/to/N0_or_Orthogroups.tsv \
    --hog True \
    --fasta_dir /path/to/fastas \
    --file_endings faa \
    --out outfile.tsv \
    --simple True

If --simple=False resulting tsv looks like this:

HOG	Best Gene Name	Gene Name Occurrences
N0.HOG0000000	amino acid ABC transporter	{JSON}
N0.HOG0000001	IS30 family transposase	{JSON}
N0.HOG0000002	IS5/IS1182 family transposase	{JSON}

The JSON is a dictionary with key='gene name' -> value=occurrence, for example:

{
  'Integrase core domain protein': 47,
  'hypothetical protein': 15,
  'IS30 family transposase': 126
}

If --simple=True resulting tsv looks like this (no header):

N0.HOG0000000	amino acid ABC transporter
N0.HOG0000001	IS30 family transposase
N0.HOG0000002	IS5/IS1182 family transposase

Usage as python class

# load class
from orthofinder_tools import OrthogroupToGeneName

PATH_TO_ORTHOFINDER_FASTAS = '/path/to/OrthoFinder/fastas'
CURRENT_FOLDER = 'Results_Mon00'

otg = OrthogroupToGeneName(
    fasta_dir=PATH_TO_ORTHOFINDER_FASTAS,
    file_endings='faa',
)
otg.load_hog(
    hog_tsv=F'{PATH_TO_ORTHOFINDER_FASTAS}/OrthoFinder/{CURRENT_FOLDER}/Phylogenetic_Hierarchical_Orthogroups/N0.tsv'
)

otg.majority_dict will be a python dict with key='orthogroup' -> value='best name', for example:

{
  'N0.HOG0000000': 'amino acid ABC transporter',
  'N0.HOG0000001': 'IS30 family transposase',
  'N0.HOG0000002': 'IS5/IS1182 family transposase',
}

otg.save_majority_df(outfile='path/to/outfile.tsv) writes the following file:

HOG Best Gene Name  Gene Name Occurrences
N0.HOG0000000   amino acid ABC transporter Counter({'amino acid ABC transporter': 43})
...

otg.save_orthogroup_to_gene_ids(outfile='path/to/outfile.tsv) writes the following file (no header):

N0.HOG0000000   gene_1  gene_2
N0.HOG0000001   gene_3  gene_4  gene_5
...

otg.save_orthogroup_to_gene_ids(outfile='path/to/outfile.tsv) writes the following file (no header):

N0.HOG0000000	amino acid ABC transporter ATP-binding protein
N0.HOG0000001	ATP-binding cassette domain-containing protein
...

orthofinder_plots

Disclaimer: This script is a port of roary_plots by Marco Galardini (marco@ebi.ac.uk).

# Command line usage:
orthofinder_plots --help
orthofinder_plots --tree data/SpeciesTree_rooted.txt --orthogroups_tsv data/Orthogroups.tsv --out output

Three files will be created:

Usage as python class

# load class
from orthofinder_tools import create_plots

create_plots(
    tree='/path/to/SpeciesTree_rooted.txt',
    orthogroups_tsv='/path/to/Orthogroups.tsv',
    format='svg',
    no_labels=False,
    out='/path/to/output/folder'
)