ADD: cluster and reverse complement correction for resfinder

BigDataBiology / argNorm

ARG normalization by mapping to the ARO ontology.

MIT License

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ADD: cluster and reverse complement correction for resfinder #38

Closed Vedanth-Ramji closed 6 months ago

Vedanth-Ramji commented 6 months ago

Resfinder has gene clusters which can't be passed through RGI using 'contig' mode.
Gene clusters were identified and were manually assigned ARO numbers.
40 gene clusters present.
9 genes in reverse complement form also present.
RC genes were all manually curated.
Delete get_data_path function

luispedro commented 6 months ago

The code for actually running rgi correctly for resfinder (and the output thereof) is still missing as well.

Vedanth-Ramji commented 6 months ago

I just added the code for using the AA version of resfinder.

It seems, however, that this could have been done without special-casing resfinder? Why is this different from the other manual curation files?

The other manual curation files are adding genes that are not present in the mapping tables (i.e. RGI can't map them automatically). The new 'correction' files are changing mappings that are already present in the mapping tables (i.e. correcting RGI as it is not detecting a gene cluster or reverse complement properly and mapping to a wrong ARO number).

luispedro commented 6 months ago

The other manual curation files are adding genes that are not present in the mapping tables (i.e. RGI can't map them automatically). The new 'correction' files are changing mappings that are already present in the mapping tables (i.e. correcting RGI as it is not detecting a gene cluster or reverse complement properly and mapping to a wrong ARO number).

I know this, but I don't see why it matters for my question. Why does the code need to special-case resfinder? Isn't this just a different way in which the files were generated, but the same code can handle both.