Synopsis

This repository contains the source code used for:

• extracting individual resolutions from the .mcool files contained in the StripeBench benchmark and adding a vector of 1.0s as weights (required for some stripe callers);
• the data analysis for the StripePy manuscript (preprint available soon).

Input data consists of:

• The StripeBench benchmark, see doi.org/10.5281/zenodo.14448329
• The real contact maps and their ground truth annotations, as detailed in the StripePy manuscript
• The output of StripePy and other stripe callers over the benchmark and maps mentioned in the previous two points, see doi.org/10.5281/zenodo.14449731

Requirements

This repository includes an environment.yml file, which contains the dependencies for the project environment.

• To create the environment, run the following command: conda env create -f environment.yml
• Activate the environment using the command: conda activate 2024-stripepy-paper

Once the repository is downloaded, the user is tasked with creating a folder named output inside it, together with a set of subfolders which are represented in the following tree:

output
├── StripeBench
│   ├── RoIs
│   ├── boxplots
│   ├── heatmaps
│   ├── medians
│   └── tables
└── real data
    ├── RoIs
    └── tables

On UNIX systems, this can be accomplished with:

mkdir -p output/StripeBench/{RoIs,boxplots,heatmaps,medians,tables} output/real\ data/{RoIs,tables}

Scripts

The following scripts can be found inside the scripts/ folder:

• preprocess_modle_matrix.py extracts individual resolutions from the .mcool files contained in the StripeBench benchmark and adds a vector of 1.0s as weights (required for some stripe callers). Example usage:

  scripts/preprocess_modle_matrix.py StripeBench/data/grch38_h1_rad21_*/*.mcool --resolutions 5000 10000 25000 50000

• run_evaluation_StripeBench.py generates Figures 3B-Q and 4, Extended Data Figures 1-3, and Tables 1-5.
• plot_RoIs_StripeBench.py generates Figure 1A.
• run_evaluation_real_data.py generates Table 6.
• plot_RoIs_real_data.py generates Figure 5.
• compare_normalizations_stripepy.py generates Table 7.
• plot_RoIs_real_data_normalizations.py generates Extended Data Figure 4.

To check the input requirements for the various script, activate the environment and then run

scripts/script_name.py --help