ajout masque

LoadPackages.R

 options(download.file.method = 'wget')
 
+
+if (!require("readr")){
+  install.packages("readr")
+}
+
+if (!require("jsonlite")){
+  install.packages("jsonlite")
+}
+
+
+if (!require("shinyFiles")){
+  install.packages("shinyFiles")
+}
+
+
 if (!require("Rcpp")){
   install.packages("Rcpp")
 }

Rfunctions/Data_Management.R

@@ -229,6 +229,129 @@ CheckTreeFile <- function(tree)
 }
 
 
+
+## Check Masque Input
+CheckMasque <- function(input,values)
+{
+  Error = NULL
+  HowTo = NULL
+ 
+  ## At least one fastq is detected
+  if(is.null(Error) && input$LoadFiles>0 && length(values$fastq_names_only)==0){
+    Error = "The selected directory must contain at least one file in the following format : fastq, fastq.gz, or fq." 
+    HowTo = "Change the working directory and check the format of the files"
+  }
+  
+  if(is.null(Error) && input$PairedOrNot=='y' && input$MatchFiles_button>0){
+    if(length(values$R2fastQ) !=length(values$R2fastQ)){
+        Error = "The number of fastq files for R1 and R2 must be the same" 
+        HowTo = "Add/Remove some files or change the suffix to identify the pairs"
+    }
+    
+    if(length(values$R2fastQ)>0  && length(values$R2fastQ)>0){
+      tmpR1 = gsub(input$R1files,x=values$R1fastQ,"") 
+      tmpR2 = gsub(input$R2files,x=values$R2fastQ,"")
+      
+      dup_files = c(values$R1fastQ[duplicated(tmpR1)],values$R2fastQ[duplicated(tmpR2)])
+      if(length(dup_files)>0){
+        Error = paste("These fastq files corresponds to the same sample names:" ,dup_files)
+        HowTo = "Change the suffix to identify the pairs"
+      }
+      
+      if(!isValidPrimer(input$R1primer)){ Error = "The primer (forward) must only contain letters from A to Z" }
+      if(!isValidPrimer(input$R2primer)){ Error = "The primer (reverse) must only contain letters from A to Z" }
+      
+    }
+    
+  }
+  if(is.null(Error) && !isValidEmail(input$to)) Error = "The email address is not valid"
+  
+  if(is.null(Error) && !isValidPrimer(input$primerSingle)){ Error = "The primer must only contain letters from A to Z" }
+  
+  if(is.null(Error)) {
+    
+    res = SamplesMasque(input,values)
+    if(length(res$samples)==0) {
+      Error = "0 sample detected"
+      if(input$PairedOrNot=='y') HowTo = "Change the working directory and/or verify the pairs matching"
+      if(input$PairedOrNot=='n') HowTo = "Change the working directory and load fastq files"
+    }
+    
+  }
+  
+  return(list(Error=Error,HowTo=HowTo))
+}
+
+
+
+isValidEmail <- function(x) {
+  grepl("\\<[A-Z0-9._%+-]+@[A-Z0-9.-]+\\.[A-Z]{2,}\\>", as.character(x), ignore.case=TRUE)
+}
+
+isValidPrimer <- function(x) {
+  !any(!grepl("[A-Z]",unlist(strsplit(x,""))))
+}
+
+
+SamplesMasque <- function(input,values)
+{
+  samples_removed = NULL
+  samples = NULL
+  
+  if(input$PairedOrNot=='y')
+  {
+    tmpR1 = gsub(input$R1files,x=values$R1fastQ,"") 
+    tmpR2 = gsub(input$R2files,x=values$R2fastQ,"")
+    
+    
+    R1samples = tmpR1[tmpR1%in%tmpR2]; R1samples_removed = values$R1fastQ[!tmpR1%in%tmpR2]
+    R2samples = tmpR2[tmpR2%in%tmpR1]; R2samples_removed = values$R2fastQ[!tmpR2%in%tmpR1]
+    
+    samples = unique(c(R1samples,R2samples))
+    samples_removed = c(R1samples_removed,R2samples_removed)
+  } else {samples = unique(values$fastq_names_only)}
+  
+  return(list(samples=samples,samples_removed=samples_removed))
+}
+
+
+
+CreateJSON <- function(input){
+  
+  tmpjson = tempfile(pattern = "file", tmpdir = "/Volumes/@home/Projets Hub/Metagenomique/meta16s/www/masque/todo",  fileext = ".json")
+  file.create(tmpjson,showWarnings=FALSE)
+  
+  if(input$PairedOrNot=='n')
+  {
+    path_fastq = paste(tempdir(),"Masque_files",sep= .Platform$file.sep)
+    df = data.frame("paired"=FALSE,
+                    "path"=path_fastq,
+                    "host"=input$HostName,
+                    "type"=input$DataTypeMasque,
+                    "mail"=input$to,
+                    "contaminant"= "/home/aghozlan/workspace/shaman_bioblend/alienTrimmerPF8contaminants.fasta"
+                    )
+
+    df %>% jsonlite::toJSON() %>% write_lines(tmpjson)
+  }
+  if(input$PairedOrNot=='y')
+  {
+    path_fastq_R1 = paste(tempdir(),"Masque_files_R1",sep= .Platform$file.sep)
+    path_fastq_R2 = paste(tempdir(),"Masque_files_R2",sep= .Platform$file.sep)
+
+    df = data.frame("paired"=FALSE,
+                    "path_R1"=path_fastq_R1,
+                    "path_R2"=path_fastq_R2,
+                    "host"=input$HostName,
+                    "type"=input$DataTypeMasque,
+                    "mail"=input$to,
+                    "contaminant"= "/home/aghozlan/workspace/shaman_bioblend/alienTrimmerPF8contaminants.fasta"
+                    )
+    df %>% jsonlite::toJSON() %>% write_lines(tmpjson)
+  }
+}
+
+
 ## Get the percentage of annotated OTU
 PercentAnnot <- function(counts,taxo)
 {

server.R

@@ -20,7 +20,7 @@ shinyServer(function(input, output,session) {
   observe(if(input$AddRegScatter) info("By adding the regression line, you will lose interactivity."))
   
   ## Reactive target
-  values <- reactiveValues(TargetWorking = target,labeled=NULL)
+  values <- reactiveValues(TargetWorking = target,labeled=NULL,fastq_names_only=NULL,R1fastQ=NULL,R2fastQ=NULL)
   
   ## Counts file
   dataInputCounts <-reactive({ 
@@ -605,24 +605,279 @@ shinyServer(function(input, output,session) {
   })
   
   
+  # ## Select a folder (for MASQUE)
+  # observeEvent(
+  #   ignoreNULL = TRUE,
+  #   eventExpr = {
+  #     input$directory
+  #   },
+  #   handlerExpr = {
+  #     # if (input$directory > 0) {
+  #       # condition prevents handler execution on initial app launch
+  #       
+  #       # launch the directory selection dialog with initial path read from the widget
+  #       path = choose.dir(default = readDirectoryInput(session, 'directory'))
+  #       
+  #       # update the widget value
+  #       updateDirectoryInput(session, 'directory', value = path)
+  #     # }
+  #   }
+  # )
+  
+  
+  #############################################################
+  ##
+  ##                        MASQUE
+  ##
+  #############################################################
   ## Select a folder (for MASQUE)
-  observeEvent(
-    ignoreNULL = TRUE,
-    eventExpr = {
-      input$directory
-    },
-    handlerExpr = {
-      if (input$directory > 0) {
-        # condition prevents handler execution on initial app launch
+  shinyDirChoose(input, 'dir', roots = c(home = '~'),filetypes = c('', 'fastq','gz','fgz'))
+  dir <- reactive(input$dir)
+  
+  output$dirSel <- renderText({ 
+    home <- normalizePath("~")
+    path_glob = file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
+  })
+  
+  path <- reactive({
+    
+    home <- normalizePath("~")
+    # file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep),"*.pdf")
+    
+   file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep),"*.f*q*")
+  })
+  
+  
+  
+  
+  # observeEvent(input$submit,{
+  #   values$fastq_names_only = NULL
+  #   tmp = tempdir()
+  #   pathTo = paste(tmp,"Masque_files",sep=.Platform$file.sep)
+  # 
+  #   if (dir.exists(pathTo))
+  #     {
+  #       file.remove(list.files(pathTo,full.names =TRUE))
+  #     } else dir.create(pathTo)
+  # 
+  #   file.copy(from=Sys.glob(path()), to=paste(tmp,"Masque_files",sep= .Platform$file.sep))
+  # })
+  # 
+  
+  observeEvent(input$submit,{
+    CMP = CheckMasque(input, values)
+    Error = CMP$Error
+    
+    if(is.null(Error))
+    {
+      tmp = tempdir()
+      home <- normalizePath("~")
+      path_glob = file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
+    
+    
+      ## Paired-end
+      if(input$PairedOrNot=="y"){
+        cmp = 0
+        nfiles = length(values$R1fastQ)+length(values$R2fastQ)
+        
+        withProgress(message = 'Uploading files...', value = 0, {
+          pathToR1 = paste(tmp,"Masque_files_R1",sep=.Platform$file.sep)
+          pathToR2 = paste(tmp,"Masque_files_R2",sep=.Platform$file.sep)
+          
+          if(dir.exists(pathToR1)){file.remove(list.files(pathToR1,full.names =TRUE))} else dir.create(pathToR1)
+          if(dir.exists(pathToR2)){file.remove(list.files(pathToR2,full.names =TRUE))} else dir.create(pathToR2)
+        
+        for(i in values$R1fastQ){file.copy(from=paste(path_glob,i,sep=.Platform$file.sep), to=paste(tmp,"Masque_files_R1",sep= .Platform$file.sep));cmp = cmp +1;incProgress(cmp/nfiles, detail = "Forward fastq files...")}
+        for(i in values$R2fastQ){file.copy(from=paste(path_glob,i,sep=.Platform$file.sep), to=paste(tmp,"Masque_files_R2",sep= .Platform$file.sep));cmp = cmp +1;incProgress(cmp/nfiles, detail = "Reverse fastq files...")}
+        })
+        
+      } else{
         
-        # launch the directory selection dialog with initial path read from the widget
-        path = choose.dir(default = readDirectoryInput(session, 'directory'))
+        cmp = 0
+        nfiles = length(values$fastq_names_only)
         
-        # update the widget value
-        updateDirectoryInput(session, 'directory', value = path)
+        withProgress(message = 'Uploading files...', value = 0, {
+            
+          pathTo = paste(tmp,"Masque_files",sep=.Platform$file.sep)
+          
+          if(dir.exists(pathTo)){file.remove(list.files(pathTo,full.names =TRUE))} else dir.create(pathTo)
+          
+          for(i in values$fastq_names_only){file.copy(from=paste(path_glob,i,sep=.Platform$file.sep), to=paste(tmp,"Masque_files",sep= .Platform$file.sep));cmp = cmp +1;incProgress(cmp/nfiles)}
+        })
       }
+      
+      ## Create JSON file
+      withProgress(message = 'Creating JSON file...',{CreateJSON(input)})
     }
-  )
+    
+  })
+  
+  
+  
+  ## FastQ list
+  output$FastQList_out <- renderUI({
+    input$LoadFiles
+    NullBox = h3(strong("0 FastQ file detected"),style="color:red;  text-align: center")
+    res = NullBox
+    
+    home <- normalizePath("~")
+    path_glob = file.path(home, paste(unlist(isolate(dir()$path[-1])), collapse = .Platform$file.sep))
+              
+    fastq_names = Sys.glob(isolate(path()))
+    
+    if(length(fastq_names)>0 && input$LoadFiles>0)
+    {
+      if(is.null(values$fastq_names_only) || length(values$fastq_names_only)==0) values$fastq_names_only = gsub(pattern = path_glob,x = fastq_names,replacement = "")
+      # res = box(title="Select your FastQ files",width = 6, status = "primary",
+      #                 selectInput("FastQList",label = "List of the fastq files in the selected directory",values$fastq_names_only,multiple =TRUE,selectize=FALSE,size = 6),
+      #            actionButton("RemoveFastQbut",'Remove file(s)',icon=icon("remove"))
+      # )
+      res =list(
+                selectInput("FastQList",label = "List of the fastq files in the selected directory",values$fastq_names_only,multiple =TRUE,selectize=FALSE,size = 6),
+                actionButton("RemoveFastQbut",'Remove file(s)',icon=icon("remove"))
+      )
+      
+    } else res = NullBox
+    
+    return(res)
+    
+  })
+  
+  
+  observeEvent(input$LoadFiles,{
+    values$fastq_names_only = NULL
+  })
+
+
+  ## Remove FastQ function
+  RemoveFastQ <-eventReactive(input$RemoveFastQbut,{
+    
+    if(length(input$FastQList)>0)
+    {
+      ind = which(values$fastq_names_only%in% input$FastQList)
+      values$fastq_names_only = values$fastq_names_only[-ind]
+      updateSelectInput(session, "FastQList","List of the fastq files in the selected directory",values$fastq_names_only)
+    }
+  })
+  
+  
+  
+  
+  
+  ## Remove FastQ
+  observeEvent(input$RemoveFastQbut,{  
+    
+    RemoveFastQ()
+    if(input$MatchFiles_button>=1) MatchFiles()
+    
+  },priority=1)
+  
+  
+  
+  ## Update R1 and R2 lists
+  MatchFiles <-reactive({
+    
+    if(length(values$fastq_names_only)>0 && input$PairedOrNot=='y')
+    {
+      indR1 = grep(input$R1files,values$fastq_names_only)
+      indR2 = grep(input$R2files,values$fastq_names_only)
+      
+      ## If some are R1 and R2, removed from both list
+      b12 = intersect(indR1,indR2)
+      if(length(b12)>0) {indR1 = indR1[-which(indR1%in%b12)]; indR2 = indR2[-which(indR2%in%b12)]}
+      
+      
+      if(length(indR1)>0 && length(indR2)>0){
+        
+        values$R1fastQ = values$fastq_names_only[indR1]
+        values$R2fastQ = values$fastq_names_only[indR2]
+        
+        ## If some are only R1 or R2
+        tmpR1 = gsub(input$R1files,x=values$R1fastQ,""); tmpR2 = gsub(input$R2files,x=values$R2fastQ,"")
+        values$R1fastQ = values$R1fastQ[tmpR1%in%tmpR2];values$R2fastQ = values$R2fastQ[tmpR2%in%tmpR1]
+
+        ## Update the files lists
+        updateSelectInput(session, "R1filesList","",values$R1fastQ); updateSelectInput(session, "R2filesList","",values$R2fastQ)
+      } else{updateSelectInput(session, "R1filesList","","");updateSelectInput(session, "R2filesList","","")}
+    } else{updateSelectInput(session, "R1filesList","","");updateSelectInput(session, "R2filesList","","")}
+  })
+  
+  
+  observeEvent(input$MatchFiles_button,{  
+    
+    MatchFiles()
+    
+  },priority=1)
+  
+  
+  
+  ## Remove FastQ function directly from R1, R2
+  RemoveFastQ_R1R2 <-eventReactive(input$RemoveFastQbut_R1R2,{
+    
+    if(length(input$R1filesList)>0)
+    {
+      ind = which(values$R1fastQ%in% input$R1filesList)
+      values$R1fastQ = values$R1fastQ[-ind]
+      updateSelectInput(session, "R1filesList","",values$R1fastQ)
+    }
+    
+    if(length(input$R2filesList)>0)
+    {
+      ind = which(values$R2fastQ%in% input$R2filesList)
+      values$R2fastQ = values$R2fastQ[-ind]
+      updateSelectInput(session, "R2filesList","",values$R2fastQ)
+    }
+    
+    
+  })
+  
+  ## Remove FastQ from R1, R2
+  observeEvent(input$RemoveFastQbut_R1R2,{  
+    
+    RemoveFastQ_R1R2()
+    
+  },priority=1)
+  
+  
+  # observe({
+  #   CMP = CheckMasque(input, values)
+  #   toggleState("submit",condition = is.null(CMP$Error))
+  # })
+  
+  observe({
+    toggleState("box-match",condition = (input$PairedOrNot=="y"))
+  })
+  
+  
+
+  output$InfoMasque<- renderUI({
+    input$submit
+    
+    CMP = isolate(CheckMasque(input, values))
+   
+    if(!is.null(CMP$Error) && input$submit>0) {
+      box(title = "Error", status = "danger",width = 12,
+          h6(strong(CMP$Error))
+      )
+    } else return(NULL)
+
+  })
+  
+  output$InfoMasqueHowTo<- renderUI({
+    input$submit
+    
+    CMP = isolate(CheckMasque(input, values))
+    
+    if(!is.null(CMP$HowTo) && input$submit>0) {
+      box(title = "How To", status = "success",width = 12,
+          h6(strong(CMP$HowTo))
+      )
+    } else return(NULL)
+    
+  })
+  
+  ######################## END MASQUE #################################
+  
   
   observeEvent(input$deleteRows,{
     

ui.R

@@ -259,12 +259,78 @@ body <- dashboardBody(
             #                      to perform to use a set of parameters already tested on serveral projects for the numerous software used to perform the clustering and the annotation.
             #                      to perform an uptodate analysis considering the scientific litterature."
                           ))),
-                      fluidRow(directoryInput('directory', label = 'select a directory')),
+            
+            hr(),
+            HTML('<center><h2 style="color:#053383;"><b>Start your analysis</b></h2></center>'),
+            hr(),
+            fluidRow(
+              column(width=2),
+              column(width=8,
+              box(title="About",width = 12, status = "primary",
+  
+                  column(width=6,  radioButtons("DataTypeMasque",label = "Type of data",choices = c("16S/18S" = "16S_18S","23S/28S" = "23S_28S","ITS" = "ITS"),inline = TRUE)),
+                  column(width=6,  radioButtons("PairedOrNot",label = "Paired-end sequencing ?",choices = c('Yes'="y","No"="n"),selected = "n",inline = TRUE)),
+                  column(width=6,  tags$div(title="Enter a valid email address to get your results",textInput("to", "Email address *", value="yyy@xxx"))),
+                  column(width=6,  selectizeInput("HostName",label = "Select the host",
+                                                  choices =   c("None"="", "a.stephensi (mosquito)" = "astephensi"," b.taurus (cow)" = "btaurus", "c.familiaris (dog)" = "cfamiliaris",
+                                                                "chiroptera (bat)" = "chiroptera", "c.sabaeus (Apes)" = "csabaeus" , "d.melanogaster (fly)"="dmelanogaster", 
+                                                                "e.caballus (Horse)" = "ecaballus", "f.catus (cat)" = "fcatus", "hg18 (human)"="hg18", "hg19 (human)"="hg19", 
+                                                                "hg38 (human)" = "hg38", "m.lucifugus (bat)" = "mlucifugus", "mm8 (mouse)"= "mm8", "mm9 (mouse)" = "mm9", 
+                                                                "mm10 (mouse)"="mm10", "p.vampyrus (bat)" = "pvampyrus", "s.scrofa (Boar)" = "sscrofa"))),
+                  column(width=6, tags$div(title="If no, default values are chosen",checkboxInput("primer", "Specify the primer"))),
+                  conditionalPanel(condition="input.primer && input.PairedOrNot=='y'",
+                                   column(width=12,
+                                     textInput("R1primer",label = "Forward primer",value = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG"),
+                                     textInput("R2primer",label = "Reverse primer",value = "GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC")
+                                   )
+                  ),
+                  conditionalPanel(condition="input.primer && input.PairedOrNot=='n'",
+                                   column(width=12,
+                                     textInput("primerSingle",label = "Primer",value = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG")
+                                   )
+                  )
+              ), 
+              
+              box(title="Directory containing the FastQ files ",width = 12, status = "primary",
+                    column(width=12,verbatimTextOutput("dirSel")),
+                    br(),
+                    column(width=12,
+                            shinyDirButton("dir", "Select a directory", "Upload",buttonType = "primary"),
+                            HTML("&nbsp;"),
+                            actionButton("LoadFiles",'Load',icon=icon("refresh"))
+                    ),
+                    conditionalPanel(condition="input.LoadFiles>=1",
+                                     br(),
+                                     hr(),
+                                     br(),
+                                      column(width=12,uiOutput("FastQList_out"))
+                                     )
+                    
+              ),
 
-                        br(),
-                        fluidRow(
-                        )
+              box(id="box-match",title=" Match the paired files (only for paired-end sequencing)",width = 12, status = "primary",
+                      column(width=6,  textInput("R1files",label = "Suffix R1 (Forward)",value = "_R1"),
+                            selectInput("R1filesList",label = "","",multiple =TRUE,selectize=FALSE)),
+                            column(width=6,  
+                                    textInput("R2files",label = "Suffix R2 (Reverse)",value = "_R2"),
+                                    selectInput("R2filesList",label = "","",multiple =TRUE,selectize=FALSE)
+                                   ),
+                            column(width=12,
+                                    actionButton("MatchFiles_button",'Match',icon=icon("exchange"),class="btn-primary",style="color: #fff;"),
+                                    HTML("&nbsp;"),
+                                    actionButton("RemoveFastQbut_R1R2",'Remove file(s)',icon=icon("remove"))
+                                  )
+              ),
+              div(style = "text-align:center;",actionButton("submit", h4(strong("Check and submit")), icon("chevron-circle-right",class="fa-2x"),class="btn-primary",style = "color: #fff"))
             ),
+            column(width=2,
+                   uiOutput("InfoMasque"),
+                   uiOutput("InfoMasqueHowTo")
+                   )
+
+          )
+            
+    ),
 
     tabItem(tabName = "Upload",
             tags$style(type='text/css', ".well { max-width: 20em; }"),