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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.
The text was updated successfully, but these errors were encountered:
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
Describe the solution you'd like
The following adjustments can help:
--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.protein_product
in the functional annotation file to have direct link for app.The text was updated successfully, but these errors were encountered: