Version 0.5.0
Updated the drug categorization and improved manual curation
USER-FACING CHANGES
Improved drug categorization
drugs_to_drug_classes()
also uses the 'has_part' ARO relationship now to get drug classes for antibiotic mixtures. In case of antibiotic mixtures, the drug classes of the drugs associated with 'has_part' are returned rather than 'antibiotic mixture' (ARO:3000707).- 'antibiotic mixture' will not be reported as a drug class, rather the individual antibiotic classes making up the antibiotic mixture will be reported.
Improved manual curation
- manual curation (argannot):
(Tet)tetH:EF460464:6286-7839:1554
was incorrectly annotated as ARO:3004797 which is a beta-lactamase due to a loose RGI hit. This was manually curated to ARO:3000175. - Improved curation:
- resfinder_curation: grdA_1_QJX10702 -> 3007380 & EstDL136_1_JN242251 -> 3000557
- megares_curation: MEG_2865|Drugs|Phenicol|Chloramphenicol_hydrolase|ESTD -> 3000557
Bugfixes
confers_resistance_to()
now gets drugs information even if it is encoded at a higher level in the ARO. For example, OXA-19 previously only returned cephalosporin and penam, but now will also return oxacillin (from AMR gene family).drugs_to_drug_classes()
now correctly only returns the immediate child of 'antibiotic molecule' as the drug class (this was previously not the case for certain corner cases).- inconsistent ARO versions deeparg, megares, resfinderfg & sarg curation: ARO:3004445 -> ARO:3005440, this was due to a change in the ARO and the ARO number for the RSA2 gene changing, but the version of ARO bundled with argNorm was out of sync.
INTERNAL CHANGES
- AROs were previously handled as integers in the
get_aro_mapping_table()
function and this posed challenges when ARO numbers such as 'ARO:0010004' (leading zeros leading to issues). To fix this, AROs are now treated as strings so leading zeros can be maintained.