Error, siempre la misma secuencia.

README.md

@@ -0,0 +1,3 @@
+# Revtrans
+
+Paquet per a la traducció reversa de pèptid a DNA tenint en compte l'ús de codons específics.

app.R

@@ -6,22 +6,24 @@ library(reversetranslate)
 ui <- fluidPage(
 
   # Application title
-  titlePanel("Reverse tranlation"),
+  titlePanel("Reverse translation"),
   
   navbarPage("Apps",
      tabPanel("Translation",
         sidebarPanel(
-          fileInput("file1", "Sube fichero mfasta", multiple = FALSE),
+          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("calab", "Analizar")
+          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=""),
-          # tags$head(tags$style(HTML("pre { white-space: pre-wrap; word-break: break-all; }"))),
+          uiOutput("seqDNAui")
-          htmlOutput("seqDNA")
         )
     ),
     tabPanel("Codon Frequency Table",
@@ -34,38 +36,86 @@ ui <- fluidPage(
 
 # Define server
 server <- function(input, output) {
-
+    obj<-reactiveValues()
-    output$seqDNA <- renderText({
+    obj$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 == ""){
-          print("Result")
+          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$new(min=0, max=length(seqs))
-          for (i in 1:length(seqs)){
-            set.seed(123)
-            seqs_DNA<-c(seqsDNA<-reverse_translate(seqs[i],spec))
-            progress$set(message = "Reverse Translating", value = i)
-          }
-          
-          paste(dataframe2fas(data.frame(names=names_seqs, 
-                                         seqs=seqs_DNA)), collapse="<br>")
         }
+        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 %>% arrange(aa)
+        spec[order(spec$aa),]
       })
     }
+    
+    output$seqDNAui<-renderUI({
+      observeEvent(input$but_an, {})
+      if (input$for_output == 1){
+        htmlOutput("seqDNA")
+      }else{
+        tableOutput("seqDNAt")
+      }
+    })
 }
 
 # Run the application