MCDP

IMPORTANT! The newer version of this tool is available here. The newer version is faster and provides additional features, such as number of shared bases test statistic, masking and context-aware modelling.

Installation

conda install mamba
mamba create -c conda-forge -c bioconda -n mcdp python=3.9 scipy pytest pytest-rerunfailures argh numpy matplotlib yaml pandas pybigwig xlrd
conda activate mcdp

Demo

cd resources/examples_github
conda activate mcdp
bash run_comparison.sh

Usage

usage: mcdp.py [-h] [-l LOG] ref_intervals query_intervals chr_sizes

MCDP: compute p-value of number of overlaps of two interval sets.

Both reference and query interval files should be tab-separated files with three columns:

    1. Chromosome name (same as in `chr_sizes` file)
    2. Begin of an interval (0-based, closed)
    3. End of an interval (0-based, open)

Intervals should be non-overlapping and disjoint (i.e. there should be a positive gap between them).
If there is no gap (or intervals are overlapping), the program will merge those intervals.

Chromosome sizes list should be tab-separated with two columns:

    1. Chromosome name
    2. Length of a chromosome

Files can contain empty lines.
    

positional arguments:
  ref_intervals      List of reference intervals
  query_intervals    List of query intervals
  chr_sizes          List of chromosome sizes

optional arguments:
  -h, --help         show this help message and exit
  -l LOG, --log LOG  Log file (default: -)

Acknowledgements

Please cite this tool as follows:

Askar Gafurov, Broňa Brejová, Paul Medvedev, Markov chains improve the significance computation of overlapping genome annotations, Bioinformatics, Volume 38, Issue Supplement_1, July 2022, Pages i203–i211, https://doi.org/10.1093/bioinformatics/btac255