Metadata-Version: 2.1
Name: pyllelic
Version: 0.1.8
Summary: Analysis of allele-specific methylation in bisulfite DNA sequencing.
Home-page: https://github.com/Paradoxdruid/pyllelic
Author: Andrew J. Bonham
Author-email: abonham@msudenver.edu
License: GPLv3
Description: # pyllelic
        
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        <p align="right">
          ⭐ &nbsp;&nbsp;the project to show your appreciation. :arrow_upper_right:
        </p>
        
        <img src="./assets/pyllelic_logo.png" width="100" height="100" style="float: left; margin-right: 10px;">
        
        **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`](https://github.com/Paradoxdruid/pyllelic/blob/master/pyllelic_notebook.md) for an interactive demonstration.
        
        ## Example exploratory use in jupyter notebook
        
        <details>
        <summary>Click to expand...</summary>
        
        ```python
            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
        ```
        
        </details>
        
        ----------------------------------
        
        ## Dependencies and Installation
        
        ### Conda environment
        
        * Create a new conda environment using python 3.7:
        
        ```bash
        conda create --name PYLLELIC python=3.7
        conda activate PYLLELIC
        ```
        
        ### Install pyllelic
        
        ```bash
        pip install pyllelic
        ```
        
        or
        
        ```bash
        git clone https://github.com/Paradoxdruid/pyllelic.git
        ```
        
        ## Authors
        
        This software is developed as academic software by [Dr. Andrew J. Bonham](https://github.com/Paradoxdruid) at the [Metropolitan State University of Denver](https://www.msudenver.edu). It is licensed under the GPL v3.0.
        
        This software incorporates implementation from [QUMA](http://quma.cdb.riken.jp), licensed under the GPL v3.0.
        
Keywords: genomics,methylation,DNA sequencing
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
