MPRAlib

MPRAlib is a Python library and CLI for processing MPRA (Massively Parallel Reporter Assay) data.

Installation

PyPI

pip install mpralib

Conda

From the bioconda channel

conda install -c bioconda mpralib

Usage

Command Line Interface

Use the mpralib command to access various functionalities.

Validate a file

MPRAlib provides a CLI tool for validating MPRA data files against supported schemas.

mpralib validate-file <schema> --input <input_file>

• <schema>: One of reporter-sequence-design, reporter-barcode-to-element-mapping, reporter-experiment-barcode, reporter-experiment, reporter-element, reporter-variant, reporter-genomic-element, reporter-genomic-variant
• <input_file>: Path to your data file (e.g., .tsv.gz, .bed.gz)

Example:

mpralib validate-file reporter-sequence-design --input data/reporter_sequence_design.example.tsv.gz

Python API

In general MPRAlib is ment to be used as a library. Please have a look at our notebook mpralib.ipynb for a more detailed example.

License

MIT License

Links

• Documentation
• Issues