revtrans/app.R

library(shiny)
library(seqRFLP)
library(reversetranslate)

# Define UI 
ui <- fluidPage(

  # Application title
  titlePanel("Reverse translation"),
  
  navbarPage("Apps",
     tabPanel("Translation",
        sidebarPanel(
          fileInput("file1", "Upload file (fasta, csv or xlsx)", multiple = FALSE),
          selectInput("spec", label = h3("Specie"), 
                      choices = list("Human" = 1, "E. Coli" = 2), 
                      selected = 1),
          actionButton("but_an", "Analize"),
          selectInput("for_output", label = h3("Output Format"), 
                      choices = list("fasta" = 1, "tabla" = 2), 
                      selected = 1),
        ),

        mainPanel(
          textAreaInput("seqText", label="Enter mFasta text", width = "100%", height = "500px", value=""),
          uiOutput("seqDNAui")
        )
    ),
    tabPanel("Codon Frequency Table",
      mainPanel(
        tableOutput("tbl")
      )
    )
  )
)

# Define server
server <- function(input, output) {
    obj<-reactiveValues()
    obj$fasta<-NULL
    obj$seqs<-NULL
    obj$names<-NULL
    
    observe({
      if (!is.null(input$file1)){ # This ensures that the reading is only tried when File selected
        if (grepl(".xlsx", input$file1$datapath)){
          file<-openxlsx::read.xlsx(input$file1$datapath)
          obj$fasta<-dataframe2fas(file)
        }else{
          if (grepl(".csv", input$file1$datapath)){
            file<-read.csv(input$file1$datapath)
            obj$fasta<-dataframe2fas(file)
          }else{
            obj$fasta<-read.fasta(input$file1$datapath)   
          }
        }
      }
    })
    
    revtrans<-eventReactive(input$but_an, {
      if (input$seqText != "" | !is.null(obj$fasta)){
        if (input$seqText == ""){
          seqs<-obj$fasta
        }else{
          seqs<-strsplit(input$seqText,"\n")[[1]]
        }
        names_seqs<-seqs[grepl("^>",seqs)]
        names_seqs<-gsub(">","", names_seqs)
        seqs<-seqs[!grepl("^>", seqs)]
        
        if(input$spec == 1){spec<-hsapien_tbl}
        if(input$spec == 2){spec<-ecoli_tbl}
        
        seqs_DNA<-c()
        progress <- shiny::Progress$new(min=0, max=length(seqs))
        for (i in 1:length(seqs)){
          set.seed(123)
          seqs_DNA<-c(seqs_DNA, reverse_translate(seqs[i],spec))
          progress$set(message = "Reverse Translating", value = i)
        }
        progress$close()
        obj$seqs<-seqs_DNA
        obj$names<-names_seqs
      }
    })
    
    output$seqDNA <- renderText({
      print(1)
      observeEvent(input$but_an, {revtrans()})
      if (!is.null(obj$seqs)){
          paste(dataframe2fas(data.frame(names=obj$names, seqs=obj$seqs)), collapse="<br>")
      }
    })
    
    output$seqDNAt <- renderTable({
      print(2)
      observeEvent(input$but_an, {revtrans()})
      if (!is.null(obj$seqs)){
          data.frame("Name"=obj$names, "Seqs"=obj$seqs)
      }
    })
    
    {
      output$tbl <- renderTable({
        if(input$spec == 1){spec<-hsapien_tbl}
        if(input$spec == 2){spec<-ecoli_tbl}
        spec[order(spec$aa),]
      })
    }
    
    output$seqDNAui<-renderUI({
      observeEvent(input$but_an, {})
      if (input$for_output == 1){
        htmlOutput("seqDNA")
      }else{
        tableOutput("seqDNAt")
      }
    })
}

# Run the application 
shinyApp(ui = ui, server = server)