Feedback from users was that genes were not specific enough in serotype_res_incidence.txt output. I changed the resistance targets of interest for other resistance databases e.g. TET expanded to TETB, TETL, TETM, TETO, TETS. Also included more that were picked up using ResFinder e.g. MPHC. These are now included in serotype_res_incidence.txt output. It might be worth thinking about whether or not users can define their own other targets of interest, but others that are not defined are picked up in the pipeline and listed in *_drug_cat_alleles.txt anyway.
Also found out from Ben that the drug category EC (which originally stood for Erythromycin/Clindamycin) now means a group of drugs, which I've specified in the readme. Here is the more detailed version:
EC Group
Drug
Abbreviation
Macrolides
Erythromycin
ERY
Lincosamides
Clindamycin
CLI
Streptogramins
Synercid
SYN
Oxazolidinones
Linezolid
LZO
It might be worth thinking about expanding those drug categories as well for the *drug_cat_alleles.txt output.
Feedback from users was that genes were not specific enough in serotype_res_incidence.txt output. I changed the resistance targets of interest for other resistance databases e.g. TET expanded to TETB, TETL, TETM, TETO, TETS. Also included more that were picked up using ResFinder e.g. MPHC. These are now included in serotype_res_incidence.txt output. It might be worth thinking about whether or not users can define their own other targets of interest, but others that are not defined are picked up in the pipeline and listed in *_drug_cat_alleles.txt anyway.
Also found out from Ben that the drug category EC (which originally stood for Erythromycin/Clindamycin) now means a group of drugs, which I've specified in the readme. Here is the more detailed version:
It might be worth thinking about expanding those drug categories as well for the *drug_cat_alleles.txt output.