Installation

1. Install the packages in requirements.txt

conda create -n cosine_fmh_env --file requirements.txt -c conda-forge -c bioconda
conda activate cosine_fmh_env

1. Install Simka:

wget https://github.com/GATB/simka/releases/download/v1.5.3/simka-v1.5.3-bin-Linux.tar.gz
tar -xvzf simka-v1.5.3-bin-Linux.tar.gz

Then, add the bin directory in the PATH. Make sure to give +x permission.

1. Install frac-kmc (a) download binaries from https://github.com/KoslickiLab/frac-kmc/tree/main/wrappers/bin (b) make sure to give +x (execution) permission. (c) add the directory in the PATH environment

Tables

After cloning this repository:

cd tables
python generate_tables.py

Figure 1

1. First obtain the data by following the instruction in fig_1/download.txt
2. Then, change fig_1/run_tools.py, where we need to write path to the files
3. Then, run the following:

cd fig_1
python run_tools.py
python plot_runtime_comparison.py

Figure 2

1. First we need to obtain the data by following the instruction in fig_2/download.txt
2. Then, extract the downloaded data in fig_2
3. For the Ecoli dataset: (a) cd fig_2/ecoli3682 (b) bash run_tools.sh (c) gunzip simka_results_*/*.gz
4. For the HMP dataset: (a) cd fig_2/hmp_gut (b) bash run_tools.sh (c) gunzip simka_results_*/*.gz
5. Make the comparisons using python comparison.py
6. Copy the files ecoli_combined, ecoli_runtime, hmp_combined, hmp_gut_runtime to fig_2/plotting
7. Plotting:

cd fig_2/plotting
python plot_results.py