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,--geneflags on any procedure - Persistent analytical records:
--persistwrites 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
License
MIT
1 maintainer
Metadata
1 maintainer
Release files for graphpop-cli 0.1.1
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