cat-merge
Details
| GitHub | monarch-initiative/cat-merge |
| Language | Python |
| Description | Tooling for merging individual source KGX files in the Monarch ingest pipeline |
Dependencies
External Dependencies
| Package | Version |
|---|---|
| python | ^3.10 |
| click | ^8 |
| pandas | >=1.4.6,<2.1.0 |
| mkdocs | ^1.3.0 |
| scipy | >=1.9,<2.0.0 |
Documentation
cat-merge
Python library for merging individual source KGX files in the Monarch Initiative ingest pipeline.
Dependencies
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'
)