Scripts to parse OrthoFinder output
The ortho_parser.py script runs a very simple parsimony gene reconstruction method to plot gene gains on a species tree.
usage: python ortho_parser.py [-h] -i INPUT -t TREE [-s SPECIES] [-r ROOT [ROOT ...]]
[-o OUTPUT] [-d THREADS]
required arguments:
-i INPUT, --input INPUT
Orthofinder output directory
-t TREE, --tree TREE Input species tree
optional arguments:
-h, --help show this help message and exit
-s SPECIES, --species SPECIES
Name of species of interest to infer gene stats on
-r ROOT [ROOT ...], --root ROOT [ROOT ...]
Where to root unrooted species tree (eg. DroMela or DroMela,EriTena)
-o OUTPUT, --output OUTPUT
Name of output dir
-d THREADS, --threads THREADS
Number of threads to run in parallel
-c CLADE [CLADE ...], --clade CLADE [CLADE ...]
Clade(s) interest to pull out OGs gained (eg. 100 or 100,153,12)