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122 lines
3.3 KiB
122 lines
3.3 KiB
library(shiny)
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library(seqRFLP)
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library(reversetranslate)
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# Define UI
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ui <- fluidPage(
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# Application title
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titlePanel("Reverse translation"),
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navbarPage("Apps",
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tabPanel("Translation",
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sidebarPanel(
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fileInput("file1", "Upload file (fasta, csv or xlsx)", multiple = FALSE),
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selectInput("spec", label = h3("Specie"),
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choices = list("Human" = 1, "E. Coli" = 2),
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selected = 1),
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actionButton("but_an", "Analize"),
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selectInput("for_output", label = h3("Output Format"),
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choices = list("fasta" = 1, "tabla" = 2),
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selected = 1),
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),
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mainPanel(
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textAreaInput("seqText", label="Enter mFasta text", width = "100%", height = "500px", value=""),
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uiOutput("seqDNAui")
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)
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),
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tabPanel("Codon Frequency Table",
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mainPanel(
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tableOutput("tbl")
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)
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)
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)
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)
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# Define server
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server <- function(input, output) {
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obj<-reactiveValues()
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obj$fasta<-NULL
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obj$seqs<-NULL
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obj$names<-NULL
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observe({
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if (!is.null(input$file1)){ # This ensures that the reading is only tried when File selected
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if (grepl(".xlsx", input$file1$datapath)){
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file<-openxlsx::read.xlsx(input$file1$datapath)
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obj$fasta<-dataframe2fas(file)
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}else{
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if (grepl(".csv", input$file1$datapath)){
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file<-read.csv(input$file1$datapath)
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obj$fasta<-dataframe2fas(file)
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}else{
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obj$fasta<-read.fasta(input$file1$datapath)
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}
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}
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}
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})
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revtrans<-eventReactive(input$but_an, {
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if (input$seqText != "" | !is.null(obj$fasta)){
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if (input$seqText == ""){
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seqs<-obj$fasta
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}else{
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seqs<-strsplit(input$seqText,"\n")[[1]]
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}
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names_seqs<-seqs[grepl("^>",seqs)]
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names_seqs<-gsub(">","", names_seqs)
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seqs<-seqs[!grepl("^>", seqs)]
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if(input$spec == 1){spec<-hsapien_tbl}
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if(input$spec == 2){spec<-ecoli_tbl}
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seqs_DNA<-c()
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progress <- shiny::Progress$new(min=0, max=length(seqs))
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for (i in 1:length(seqs)){
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set.seed(123)
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seqs_DNA<-c(seqs_DNA, reverse_translate(seqs[i],spec))
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progress$set(message = "Reverse Translating", value = i)
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}
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progress$close()
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obj$seqs<-seqs_DNA
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obj$names<-names_seqs
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}
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})
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output$seqDNA <- renderText({
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print(1)
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observeEvent(input$but_an, {revtrans()})
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if (!is.null(obj$seqs)){
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paste(dataframe2fas(data.frame(names=obj$names, seqs=obj$seqs)), collapse="<br>")
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}
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})
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output$seqDNAt <- renderTable({
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print(2)
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observeEvent(input$but_an, {revtrans()})
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if (!is.null(obj$seqs)){
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data.frame("Name"=obj$names, "Seqs"=obj$seqs)
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}
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})
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{
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output$tbl <- renderTable({
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if(input$spec == 1){spec<-hsapien_tbl}
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if(input$spec == 2){spec<-ecoli_tbl}
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spec[order(spec$aa),]
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})
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}
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output$seqDNAui<-renderUI({
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observeEvent(input$but_an, {})
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if (input$for_output == 1){
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htmlOutput("seqDNA")
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}else{
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tableOutput("seqDNAt")
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}
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})
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}
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# Run the application
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shinyApp(ui = ui, server = server)
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