Methtools

Methtools is a Python toolkit for methylation analysis, providing command-line tools and API utilities for handling Whole Genome Bisulfite Sequencing (WGBS) and Oxford Nanopore Technologies (ONT) methylation data.

Installation

1. Clone the repository:

   git clone https://github.com/m-mahgoub/methtools.git
   cd methtools

2. Install dependencies: It is recommended to use a virtual environment.

   python -m venv venv
   source venv/bin/activate  # On Windows use `venv\\Scripts\\activate`
   pip install -r requirements.txt

3. Install Methtools:

   pip install .

   Or for development (editable install):

   pip install -e .

After installation, the methtools command should be available in your terminal.

Prerequisite Tools

Methtools requires the following command-line tools to be installed and available in your PATH:

• Samtools (minimum version 1.9)
• Modkit (minimum version 0.1.10)
• Bedtools (minimum version 2.31.1)

Ensure these tools are installed and meet the minimum version requirements before running workflows.

Command-Line Interface (CLI)

Methtools offers the following command-line tools:

1. snpsplit

Splits BAM/CRAM files based on SNP information. This is useful for separating reads based on haplotype.

Example:

methtools snpsplit \
    --bam-path input.bam \
    --ref-fasta reference.fasta \
    --vcf-path variants.vcf \
    --regions-path regions.bed \
    --results-path ./snpsplit_results \
    --out-prefix mysnpsplit

2. readmeth

Extracts read-level methylation data from BAM files.

Example:

methtools readmeth \
    --bam hap1.bam,hap2.bam \
    --haplotypes HAP1,HAP2 \
    --out-file methylation_calls.tsv \
    --regions-bed regions_to_analyze.bed \
    --sample MySample

Example (single BAM):

methtools readmeth \
    --bam merged_sample.bam \
    --out-file methylation_calls.tsv \
    --regions-bed regions_to_analyze.bed \
    --sample MySample

3. call-mhb

Calls Methylation Haplotype Blocks (MHBs) from BAM files or precomputed methylation call files. Currently, it supports only Oxford Nanopore Technologies (ONT) data.

Note: When running call_mhb with BAM files (using the --bam option), samtools (>=1.9) and modkit (>=0.1.10) must be installed and available in your system's PATH. These tools are used for processing BAM files and extracting methylation calls.

Example (from BAM files):

methtools call-mhb \
    --bam input1.bam,input2.bam \
    --fasta reference.fasta \
    --regions regions_for_mhb.bed \
    --cpgs all_cpg_sites.bed \
    --output-dir ./mhb_output \
    --threads 4 \
    --output-prefix my_mhb_run \
    --output-formats tsv,bed

Example (from precomputed methylation calls):

methtools call-mhb \
    --methylation-calls precomputed_calls.tsv \
    --regions regions_for_mhb.bed \
    --cpgs all_cpg_sites.bed \
    --output-dir ./mhb_output \
    --threads 4 \
    --output-prefix my_mhb_run_precomputed

API Utilities

Methtools also provides underlying Python modules and functions that can be imported and used in custom scripts for more advanced or specific methylation data analyses. These can be found within the methtools.