gtedemedtest

This repository contains data and script for reproducing results in the follow manuscript:

The Effect of Genome Graph Expressiveness onthe Discrepancy Between Genome Graph Distanceand String Set Distance

plot_GTED_EMED.ipynb contains necessary scripts to analyze results presented in the manuscript scripts/ contains necessary scripts to

1. Sample flow decomposition from input graphs
2. Compute FGTED between graphs
3. Construct MSA/dBG graphs with conforming formats to FGTED solver

How to compute FGTED / sample diameters from different data

• See pipeline_tcr.sh, pipeline_hbv.sh for scripts to produce pair-wise FGTED.
• See pipeline_diameter.sh for scripts to produce sampled diameters.

Data

T-Cell Receptor

• Data: MSA graph and dBG4 constructed on 50 string sets are contained in TCR_graphs
  • The instruction to simulate TCR repertoires is included in data/
  • TCR_all_EMED.csv -- contains all pair-wise EMED
  • TCR_sampled_diameters_msa.csv -- contains all sampled diameters on MSA graphs
  • TCR_sampled_diameters_dbg4.csv -- contains all sampled diameters on dBG4 graphs
  • TCR_fgted_logs -- contains all output from gurobi for solving FGTED
  • TCR_summary.csv -- contains summary stats for all pairs of MSA graphs
  • TCR_FGTED.csv -- contains FGTED between pairs of dBG4 graphs

Hepatitis B Virus

• Data: MSA graphs constructed on 9 string sets are contained in HBV_graphs
  • HBV_all_EMED.csv -- contains all pair-wise EMED
  • HBV_sampled_diameters.txt -- contains all sampled diameters
  • HBV_fgted_logs -- contains all output from gurobi for solving FGTED
  • HBV_summary.csv -- contains all summary stats for all pairs
• Scripts: see pipeline_hbv.sh for scripts to produce pair-wise FGTED
  • see GTED_MSA_HBV_solver.py for details