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import_orthofinder

The output of OrthoFinder needs to be processed for Arx. This script creates two files:

  • annotation-descriptions/OL.tsv: maps orthologs to the most common gene name
  • orthologs/orthologs.tsv: maps orthologs to genes

Usage

export FOLDER_STRUCTURE=/path/to/folder_structure
import_orthofinder --which hog

Parameters

  • --which: Type of orthogroups to import - hog for hierarchical orthogroups or og for regular orthogroups

Output Files

annotation-descriptions/OL.tsv

Maps orthologs to the most common gene name, i.e. OG0000005 → MFS transporter

orthologs/orthologs.tsv

Maps orthologs to genes, i.e. OG0000005 → STRAIN1_000069, STRAIN2_000128, STRAIN2_000137

Next Steps

Once these files exist, run the following command from within the Arx docker container:

python manage_arx.py import-orthologs

Help

import_orthofinder --help