Skip to content

Tooling for merging individual source KGX files in the Monarch ingest pipeline

Notifications You must be signed in to change notification settings

monarch-initiative/cat-merge

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

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'
)

About

Tooling for merging individual source KGX files in the Monarch ingest pipeline

Resources

Stars

Watchers

Forks

Packages

No packages published

Languages