pyllelic 0.2.4

Analysis of allele-specific methylation in bisulfite DNA sequencing.

pyllelic

⭐   the project to show your appreciation. :arrow_upper_right:

pyllelic: a tool for detection of allelic-specific methylation variation in bisulfite DNA sequencing files.

Pyllelic documention is available at https://paradoxdruid.github.io/pyllelic/ and see pyllelic_notebook.ipynb for an interactive demonstration.

Example exploratory use in jupyter notebook

    from pyllelic import pyllelic

    config = pyllelic.configure(  # Specify file and directory locations
        base_path="/Users/abonham/documents/test_allelic/",
        prom_file="TERT-promoter-genomic-sequence.txt",
        prom_start="1293200",
        prom_end="1296000",
        chrom="5",
        offset=1298163,
    )

    files_set = pyllelic.make_list_of_bam_files(config)  # finds bam files

    # Run pyllelic; make take some time depending on number of bam files
    data = pyllelic.GenomicPositionData(config=config, files_set=files_set)

    positions = data.positions

    cell_types = data.cell_types

    means_df = data.means

    modes_df = data.modes
    
    diff_df = data.diffs

    individual_data = data.individual_data

    data.save("output.xlsx")  # save methylation results

    data.save_pickle("my_run.pickle")  # save data object for later analysis
    
    data.write_means_modes_diffs(filename="Run1_")  # write output data files

    data.histogram("CELL_LINE", "POSITION")  # visualize data for a point

    data.heatmap(min_values=1)  # methylation level heatmap

    data.quma_results["CELL_LINE"]  # see summary data for a cell line

---

Dependencies and Installation

Conda environment

Create a new conda environment using python 3.7:

conda create --name PYLLELIC python=3.7
conda activate PYLLELIC

Install pyllelic

pip install pyllelic

or

git clone https://github.com/Paradoxdruid/pyllelic.git

Authors

This software is developed as academic software by Dr. Andrew J. Bonham at the Metropolitan State University of Denver. It is licensed under the GPL v3.0.

This software incorporates implementation from QUMA, licensed under the GPL v3.0.