GraphPop CLI

Command-line interface for GraphPop — a graph database-native population genomics engine that reduces summary statistic complexity from O(V×N) to O(V×K), independent of sample count.

Quick Start

pip install graphpop-cli
graphpop setup --password mypass    # Downloads Neo4j + procedures plugin
graphpop start                      # Start the database

Prerequisites: Python 3.10+, Java 21+ (for Neo4j runtime).

Features

• 60 commands across 11 functional domains
• 12 population genetics procedures: diversity, Fst, SFS, iHS, XP-EHH, nSL, ROH, Garud's H, LD, genome scan, pop summary, joint SFS
• Annotation conditioning: --consequence, --pathway, --gene flags on any procedure
• Persistent analytical records: --persist writes results to graph nodes
• Publication-ready plots: 11 visualization types following Nature Methods guidelines

Usage

# Population diversity
graphpop diversity chr1 1 50000000 EUR -o diversity.tsv

# Annotation-conditioned analysis
graphpop diversity chr1 1 43270923 GJ-tmp --consequence missense_variant

# Selection scan
graphpop ihs chr22 EUR --persist -o ihs.tsv

# Multi-statistic convergence
graphpop converge --stats ihs,xpehh,h12 --thresholds 2,2,0.3 --pop EUR

Documentation

• Full documentation
• Rice 3K vignette
• Human 1000G vignette

License

MIT