ENH: Improve mapping accuracy of normalizers by making the preprocessing of input genes and reference genes more precise #84
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…ing of input genes and reference genes more precise Previously, for resfinder and ncbi genes, input ids were processed by just using gene symbols. However, several genes can have the same gene_symbol. For example, tet(O/32/O)_1_JQ740052, tet(O/32/O)_2_AJ295238, and tet(O/32/O)_3_NZ_AUJS01000017 all have the same gene_symbol—tet(O/32/O). While tet(O/32/O)_1_JQ740052 and tet(O/32/O)_2_AJ295238 are mapped to ARO:3007119, tet(O/32/O)_3_NZ_AUJS01000017 is mapped to ARO:3000190. To solve this, I've included the reference accessions (e.g. AJ295238) in the preprocessing step for input ids from the resfinder and ncbi databases in ResFinderNormalizer, AMRFinderPlusNormalizer, and AbricateNormalizer. Exact changes to processing: Resfinder database: - ResFinderNormalizer: Changed preprocessing of input ids to concate entries from `gene_name` & `reference_accession` for hamronized results and `Resistance gene` & `Accession no.` for raw results. - AbricateNormalizer: Changed preprocessing of input ids to concatenate entries from `gene_name` and `reference_accession` for hamronized results and `GENE` and `ACCESSION` for raw results. NCBI database: - AMRFinderPlusNormalizer: Changed preprocessing of input ids to concatenate entries from `gene_name` and `reference_accession` for hamronized results & `Sequence name` and `Accession of closest sequence` for raw results. - AbricateNormalizer: Changed preprociess of input ids to procure entries from `gene_name` for hamronized results and `PRODUCT` from raw results. Reference genes from the `resfinder` and `ncbi` databases are now processed to match these new input genes.
luispedro
requested changes
Feb 4, 2025
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I just saw that I can cut down looping in the abricate normalizer as well. I'll just get that as well and rebase, so it'll be included in the latest commit. |
…gene preprocessing Cutting down unnecessary looping throughout input and reference genes.
Vedanth-Ramji
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Previously, for resfinder and ncbi genes, input ids were processed by just using gene symbols. However, several genes can have the same gene_symbol. For example,
tet(O/32/O)_1_JQ740052,tet(O/32/O)_2_AJ295238, andtet(O/32/O)_3_NZ_AUJS01000017all have the same gene_symbol—tet(O/32/O). Whiletet(O/32/O)_1_JQ740052andtet(O/32/O)_2_AJ295238are mapped toARO:3007119,tet(O/32/O)_3_NZ_AUJS01000017is mapped toARO:3000190. To solve this, I've included the reference accessions (e.g. AJ295238) in the preprocessing step for input ids from the resfinder and ncbi databases in ResFinderNormalizer, AMRFinderPlusNormalizer, and AbricateNormalizer.Exact changes to processing:
Resfinder database:
gene_name&reference_accessionfor hamronized results andResistance gene&Accession no.for raw results.gene_nameandreference_accessionfor hamronized results andGENEandACCESSIONfor raw results.NCBI database:
gene_nameandreference_accessionfor hamronized results &Sequence nameandAccession of closest sequencefor raw results.gene_namefor hamronized results andPRODUCTfrom raw results.Reference genes from the
resfinderandncbidatabases are now processed to match these new input genes.