methpype is a python package for processing Illumina methylation array data. View on ReadTheDocs.

Linux/OSX Windows

The MethPype package contains both high-level APIs for processing data from local files and low-level functionality allowing you to customize the flow of data and how it is processed.

MethPype maintains configuration files for your Python package manager of choice: conda, pipenv, and pip.

pip install methpype

The primary Methpype API provides methods for the most common data processing and file retrieval functionality.

Run the complete methylation processing pipeline for the given project directory, optionally exporting the results to file.

Returns: A collection of DataContainer objects for each processed sample

from methpype import run_pipeline

data_containers = run_pipeline(data_dir, array_type=None, export=False, manifest_filepath=None, sample_sheet_filepath=None, sample_names=None)

Methpype provides a command line interface (CLI) so the package can be used directly in bash/batchfile scripts as part of building your custom processing pipeline.

All invocations of the MethPype CLI will provide contextual help, supplying the possible arguments and/or options available based on the invoked command. If you specify verbose logging the package will emit log output of DEBUG levels and above.

>>> python -m methpype

usage: methpype [-h] [-v] {process,sample_sheet} ...

Utility to process methylation data from Illumina IDAT files

positional arguments:
  {process,sample_sheet}
    process             process help
    sample_sheet        sample sheet help

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         Enable verbose logging

The MethPype cli provides two top-level commands:

• process to process methylation data
• sample_sheet to find/read a sample sheet and output its contents

Process the methylation data for a group of samples listed in a single sample sheet.

If you do not provide the file path for the project's sample_sheet the module will try to find one based on the supplied data directory path. You must supply either the name of the array being processed or the file path for the array's manifest file. If you only specify the array type, the array's manifest file will be downloaded from a Life Epigenetics archive.

>>> python -m methpype process

usage: methpype idat [-h] -d DATA_DIR [-a {custom,450k,epic,epic+}]
                     [-m MANIFEST] [-s SAMPLE_SHEET]
                     [--sample_name [SAMPLE_NAME [SAMPLE_NAME ...]]]
                     [--export]

Process Illumina IDAT files

optional arguments:
  -h, --help            show this help message and exit
  -d, --data_dir        Base directory of the sample sheet and associated IDAT
                        files
  -a, --array_type      Type of array being processed
                        Choices: {custom,450k,epic,epic+}
  -m, --manifest        File path of the array manifest file
  -s, --sample_sheet    File path of the sample sheet
  --sample_name         Sample(s) to process
  --export              Export data to csv

Find and parse the sample sheet in a given directory and emit the details of each sample. This is not required for actually processing data.

>>> python -m methpype sample_sheet

usage: methpype sample_sheet [-h] -d DATA_DIR

Process Illumina sample sheet file

optional arguments:
  -h, --help            show this help message and exit
  -d, --data_dir        Base directory of the sample sheet and associated IDAT
                        files

These are some functions that you can use within methpype. run_pipeline calls them for you as needed.

Find and parse the sample sheet for the provided project directory path.

Returns: A SampleSheet object containing the parsed sample information from the project's sample sheet file

from methpype import get_sample_sheet

sample_sheet = get_sample_sheet(dir_path, filepath=None)

Find and parse the manifest file for the processed array type.

Returns: A Manifest object containing the parsed probe information for the processed array type

from methpype import get_manifest

manifest = get_manifest(raw_datasets, array_type=None, manifest_filepath=None)

Find and parse the IDAT files for samples within a project's sample sheet.

Returns: A collection of RawDataset objects for each sample's IDAT file pair.

from methpype import get_raw_datasets

raw_datasets = get_raw_datasets(sample_sheet, sample_names=None)