README.md

cat-merge

Python library for merging individual source KGX files in the Monarch Initiative ingest pipeline.

Dependencies

• Poetry
• Pandas

Usage

Import the merge tool:

from cat_merge.merge import merge

You can either merge a list of node and edge files:

merge(
    name='monarch-kg',
    nodes=['xenbase_gene_nodes.tsv','reactome_pathway_nodes.tsv','monarch_ontology_nodes.tsv'],
    edges=['xenbase_gene_to_phenotype_edges.tsv','monarch_ontology_edges.tsv']
)

Or merge an entire directory:

merge(
    name='monarch-kg',
    input_dir='transform_output',
    output_dir='merged-output'
)