pyllelic 0.1.6

Analysis of allele-specific methylation in bisulfite DNA sequencing.

pyllelic

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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:

Click to expand...

    import pyllelic

    pyllelic.set_up_env_variables(  # Specify file and directory locations
        base_path="/Users/abonham/documents/test_allelic/",
        prom_file="TERT-promoter-genomic-sequence.txt",
        prom_start="1293000",
        prom_end="1296000",
        chrom="5",
    )

    pyllelic.setup_directories()  # Read env variables to set up directories to use

    files_set = pyllelic.make_list_of_bam_files()  # finds bam files

    positions = pyllelic.index_and_fetch(files_set)  # index bam and creates bam_output folders/files

    pyllelic.genome_parsing()  # writes out genome strings in bam_output folders

    cell_types = pyllelic.extract_cell_types(files_set)  # pulls out the cell types available for analysis

    df_list = pyllelic.run_quma_and_compile_list_of_df(cell_types, filename)  # run quma, get dfs

    means_df = pyllelic.process_means(df_list, positions, files_set)  # process means data from dataframes

    modes_df = pyllelic.process_modes(df_list, positions, cell_types)  # process modes data from dataframes

    diff_df = pyllelic.find_diffs(means_df, modes_df)  # find difference between mean and mode

    pyllelic.write_means_modes_diffs(means_df, modes_df, diffs_df, filename)  # write output data to excel files

    final_data = pyllelic.pd.read_excel(pyllelic.config.base_directory.joinpath(filename), dtype=str, index_col=0, engine="openpyxl")  # load saved data

    individual_data = pyllelic.return_individual_data(df_list, positions, files_set)  # load individual data sets

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

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

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Dependencies and Installation

Conda environment

• Create a new conda environment using python 3.7:

conda create --name methyl python=3.7
conda activate methyl
conda config --env --add channels conda-forge

Install pyllelic

pip install pyllelic

or

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

Install python dependencies (not needed if installed via pip install pyllelic)

conda install pandas numpy scipy plotly dash notebook xlsxwriter xlrd openpyxl tqdm biopython ipywidgets
conda install -c bioconda samtools pysam scikit-bio
conda install -c conda-forge jupyter_contrib_nbextensions

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.