Update scripts to accomodate re-organized pokay

[anwarMZ]

Is your feature request related to a problem? Please describe.
Pokay has been updated to host other priority pathogens in addition to SARS-CoV-2 data. We need to update the script: functional_annotation.py that digests pokay literature and fill in the functional annotation template.

Currently, the script takes two arguments

        description='This script produces a TSV file from TXT files '
                    'in POKAY  '
                    'https://github.com/nodrogluap/pokay/tree/master'
                    '/data for annotating SARS-COV-2 mutations')
    parser.add_argument('--inputdir', type=str, default=None,
                        help='directory path for input files')
    parser.add_argument('--outputfile', type=str, default=None,
                        help='output file (.TSV) format')
 

Describe the solution you'd like
The following adjustments can help:

• Add an argument to specify the accession id e.g., --accession NC_045512 for sars-cov-2 and --accession NC_063383` for mpox. If --accession is None (default). This would require another CSV file with custom functions. When accession is provided, the workflow will use the current versioned functional annotation.
• Need a dictionary to connect protein products with genes and prefixes in the filenames in literature
• Add a column of protein_product in the functional annotation file to have direct link for app.

[miseminger]

Only read CDS_mature_peptides from the JSON for the protein_product