Mercurial > repos > nml > mykrobe_parser

diff mykrobe_parser.R @ 5:deebc6410d13 draft

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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit bbf7dd6b56e8ee77cff1f98a42a5abadd681b7ac
author nml
date Thu, 09 May 2019 14:16:34 -0400
parents 8529045f0fdf
children 8e7e5a660942
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--- a/mykrobe_parser.R	Thu Apr 25 10:13:46 2019 -0400
+++ b/mykrobe_parser.R	Thu May 09 14:16:34 2019 -0400
@@ -291,7 +291,7 @@
         mutate(variants = strsplit(variants, "__")) %>% # Split the mutations across rows (list first then split across rows)
         unnest(variants) %>% 
         separate(variants, c("gene", "mutation"), "_") %>% 
-        mutate(columnname = ifelse(gene %in% c("tlyA", "rrs", "eis", "gid"), # Check for columns that include the drug name or not and paste accordingly
+        mutate(columnname = ifelse(gene %in% c("gyrA", "tlyA", "rrs", "eis", "gid"), # Check for columns that include the drug name or not and paste accordingly
                                    paste("Mykrobe", drug, gene, sep = "_"),
                                    paste("Mykrobe", gene, sep = "_"))) %>% 
         # Extract out the mutation information with a regex that covers all potential genes