convert everything to uppercase.

ONATRY-CIT/app.R

@@ -23,6 +23,7 @@ server <- function(input, output) {
   
     process<-eventReactive(input$submit, {
       fa=input$query
+
       
       fasplit<-strsplit(gsub("^>","",fa), ">")[[1]]
       txtQuery<-c()
@@ -34,7 +35,7 @@ server <- function(input, output) {
       }
       names(txtQuery)<-names
       
-      txtQuery<-gsub("\n","",txtQuery)
+      txtQuery<-toupper(gsub("\n","",txtQuery))
       dnaQuery<-DNAStringSet(txtQuery)
       
       Query<-codonTable(dnaQuery)
@@ -126,6 +127,7 @@ server <- function(input, output) {
         mutate(Weight=Usage/max(Usage))
       
       Query_codons<-sapply(txtQuery, function(x) substring(x,seq(1,(nchar(x)-2),3), seq(3,nchar(x),3)))
+      
       Query_CAI<-do.call(rbind, lapply(names(Query_codons), function(x){
         merge(
           data.frame(Position=1:length(Query_codons[[x]]),
@@ -134,7 +136,7 @@ server <- function(input, output) {
           w[,c("Codon","AA","Weight")]
         ) %>% arrange(Position)
       }))
-      
+
       Query_CAI[Query_CAI$AA %in% c("Met","End","Trp"),"Weight"]<-0
       
       #CAI