marcelcosta/ONATRY-CIT
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convert everything to uppercase.

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marcelcosta
2024-11-25 11:51:55 +01:00
parent c4953ec652
commit 64a3245924
1 changed files with 4 additions and 2 deletions
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ONATRY-CIT/app.R
+3 -1
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@@ -24,6 +24,7 @@ server <- function(input, output) {
process<-eventReactive(input$submit, { process<-eventReactive(input$submit, {
fa=input$query fa=input$query
fasplit<-strsplit(gsub("^>","",fa), ">")[[1]] fasplit<-strsplit(gsub("^>","",fa), ">")[[1]]
txtQuery<-c() txtQuery<-c()
names<-c() names<-c()
@@ -34,7 +35,7 @@ server <- function(input, output) {
} }
names(txtQuery)<-names names(txtQuery)<-names
txtQuery<-gsub("\n","",txtQuery) txtQuery<-toupper(gsub("\n","",txtQuery))
dnaQuery<-DNAStringSet(txtQuery) dnaQuery<-DNAStringSet(txtQuery)
Query<-codonTable(dnaQuery) Query<-codonTable(dnaQuery)
@@ -126,6 +127,7 @@ server <- function(input, output) {
mutate(Weight=Usage/max(Usage)) 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_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){ Query_CAI<-do.call(rbind, lapply(names(Query_codons), function(x){
merge( merge(
data.frame(Position=1:length(Query_codons[[x]]), data.frame(Position=1:length(Query_codons[[x]]),