Heritability Illustrator v1.0.0

Résumé fourni par la source

Gene-Level SNP Grouping, Insertion Mapping & Heritability Toolkit A small toolkit for: Extracting SNPs for arbitrary gene regions from large HapMap/VCF files Collapsing diploid calls to haploid representations and dominant genotypes Grouping strains by identical SNP‐match profiles (network-based clustering) Visualising representative strain sets and match tables as heat-map PNGs and circos plotting The code was developed for Bacillus subtilis genome‐wide association analyses but is file-format-agnostic and should work with any species as long as your HapMap/VCF files follow standard conventions. Repository layout . ├── conftest.py ├── heritability_illustrator │ ├── __init__.py │ ├── class_analysis.py # Class/phenotype group analysis helpers │ ├── convert_vcf.py # Core VCF parsing and normalization │ ├── create_gene_region_profile.py # SNP extraction for gene/region intervals │ ├── create_visualization.py # Heatmap + profile visualization pipeline │ ├── data_loaders.py # File I/O utilities for VCF and metadata │ ├── df_helpers.py # Pandas dataframe cleaning / merging │ ├── dominant_matching.py # Collapse genotypes to dominant matches │ ├── haploid_squashing.py # Convert diploid calls to haploid reps │ ├── heterozygote_to_homozygote.py # Handle heterozygous calls simplification │ ├── load_and_extract_data.py # High-level data extraction orchestration │ ├── network_helpers.py # Graph/network SNP clustering functions │ ├── plot_images.py # Matplotlib/seaborn visualization wrappers │ └── utils.py # Small utility functions ├── notebooks │ └── example_notebook.ipynb # Walkthrough notebook ├── README.md └── requirements.txt Installation 1. Clone and create an environment git clone https://github.com/LaneMatthewJ/heritability_illustrator.git cd heritability_illustrator python -m venv .venv # or conda create -n genekit python=3.11 source .venv/bin/activate or with conda: conda create -n genekit python=3.11 conda activate genekit 2. Istall Python Requirements: pip install -r requirements.txt Note: There may be a potential optional dependency: sudo apt-get install wkhtmltopdf Example Usage import heritability_illustrator from heritability_illustrator.create_visualization import generate_profile_from_vcf, create_start_stop_df start_pos = 0 stop_pos = 4_200_000 outfiles_ronn1_ME = generate_profile_from_vcf( "../variant_mapping/Bsubtilis_350strain_SNPs_final.vcf", start_pos = start_pos, stop_pos = stop_pos, class_encoding_filename = None, # '../image_data/sorted/class_encodings.xlsx' input_image_directory = None) create_start_stop_df(outfiles_ronn1_ME[0], start_pos, stop_pos, "Bsubtilis_SNPs", 0) df = pd.read_csv("Bsubtilis_350strain_SNPs_final_0_to_4200000_visualizations/Bsubtilis_350strain_SNPs_final_0_4200000_snp_matchings_by_group.tsv", sep='\t', index_col=0) data = df[df.columns[:-1]].loc[df.index[1:]] colors = ['cyan', 'black'] black_to_blue_cmap = LinearSegmentedColormap.from_list('black_to_blue', colors) sns.heatmap(data, cmap=black_to_blue_cmap) Example Applications Mapping gene-level SNP differences between experimental strains. Identifying strain clusters with identical genomic variation patterns. Performing heritability-informed grouping of phenotypes vs. genotypes. Generating publication-ready heatmaps and circos plots.

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.