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Description:

orthofindertools 0.0.2

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'
)