A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
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Update scripts to accomodate re-organized pokay #142
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 --accessionNC_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.
[x] 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.
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.