methylation_vs_transcription Python3 script

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This script was designed for the project:
"Epigenetic background of lineage-specific genome expression landscapes 
of four Staphylococcus aureus hospital isolates"
Author: Oleg Reva (oleg.reva@up.ac.za)
Last update: January 23, 2024

Usage: python3 /path/run.py [-argument option, ...]
Run the script without any arguments to display a command prompt menu
Output files will be stored into the directory output/'project_name'

Arguments:
    -h    Show this help text
    -p    Project sub-directory in the 'input' directory
    -i    Input sub-subdirectory with GFF files containing nucleotide 
        methylation data generated by the program ipdSummary
        This sub-directory must be located in the project directory (option -p)
        Default: 'GFF'
    -g    Input sub-subdirectory with GBK files of annotated genomes
        This sub-directory must be located in the project directory (option -p)
        Default: 'GBK'
    -t    Input sub-subdirectory with transcription data (RPKM) files
        This sub-directory must be located in the project directory (option -p)
        Default: 'RPKM'
    -f    Input sub-subdirectory containing the file COG.txt
        This sub-directory must be located in the project directory (option -p)
        By default this option is empty. COG.txt is expected in the project directory.
    -k    Categories of gene regulation: 'Expression categories' | 'Regulation categories'
        Default: 'Expression categories'
    -n    Number of categories (positive integer > 1)
        Default: 6
    -c    Cut-off methylation score value (positive integer)
        Default: 20
    -1    Sliding window start location relatively to transcription start sites (TSS)
        can be a positive or negative integer
        Default: -360
    -2    Sliding window end location relatively to transcription start sites (TSS)
        (can be a positive or negative integer)
        Default: 180
    -w    Sliding window width (positive integer)
        Default: 36
    -s    Sliding window step (positive integer)
        Default: 9
    -d    Smoothing sliding windows, can take values 0,1,2
        0 - no intermediate windowa
        1 - two intermediate windows with a shift -u
        2 - five intermediate windows with a shif -u
        Default: 1
    -u    Smoothing shift step (positive integer), used when -d > 0
        Default: 2
    -o    Cut-off p-values (positive floating-point number)
        Default: 0.05
    -m    Methylation type: 'A', 'C', 'm6A', 'm4C', 'm5C'
        Default: 'A'
    -z    Save regulated genes: "All" | 'No' | 'Reg'
        Save a text output file. In the current version, there is no difference between 'All' and 'Reg'
        Default: 'All'
    -a    Graph color scheme: first color for bars with negative LD, second for positive LD
        Default: 'cornflowerblue,gold'
        A graph will be shown only if the matplotlib Python module is installed