app.R

if(!require(shiny)){
    install.packages("shiny")
    library(shiny)
}
if(!require(shinyBS)){
    install.packages("shinyBS")
    library(shinyBS)
}

ui <- fluidPage(
  
  titlePanel("PyFFAME config file creator"),
  sidebarLayout(
    sidebarPanel(
      actionButton("create_file", 
                   "Create config file", 
                   class = "btn-primary"),
      tags$hr(),
      downloadButton("download_file", 
                   "Download config file", 
                   class = "btn-primary")
    ),
    mainPanel(
      textInput("in_vcf", "VCF-like input file"),
      bsTooltip("in_vcf", "Path to input file in vcf format (columns: CHROM, POS, ID, REF, ALT); leave blank if none is used."),
      textInput("in_sequence", "Sequence input file"),
      bsTooltip("in_sequence", "Path to input file containing additional sequences (columns: ID, FEATURE_SEQ); leave blank if none is used."),
      textInput("in_barcode", "Barcode input file"),
      bsTooltip("in_barcode", "Path to input file (without header) containing sufficient barcodes for the planned design."),
      radioButtons("in_barcode_type", "Barcode input file type",
                  choices=c(".json", ".txt")),
      bsTooltip("in_barcode_type", "File type of barcode input file (json format or plain text with one barcode per line)."),
      textInput("db_genome", "Genome input file"),
      bsTooltip("db_genome", "Path to reference genome file in FASTA format."),
      textInput("de_order", "Design order"),
      bsTooltip("de_order", "Design order, given as a string containing the letters 'a' to 'e' (e.g. abcde); see readme for a more in-depth explanation."),
      textInput("de_seq_1", "Added sequence 1"),
      bsTooltip("de_seq_1", "First added sequence, e.g. 5' of the feature."),
      textInput("de_seq_2", "Added sequence 2"),
      bsTooltip("de_seq_2", "Second added sequence, e.g. spacer between feature and barcode."),
      textInput("de_seq_3", "Added sequence 3"),
      bsTooltip("de_seq_3", "Third added sequence, e.g. 3' of the feature/barcode."),
      numericInput("set_feature_size", "Feature size per side",
                   value=85),
      bsTooltip("set_feature_size", "Nucleotides to add to each side of the variant (e.g., 85 will yield a total feature size of 171 nt)."),
      radioButtons("set_all_features", "Create all allelic features?",
                   choices=c("Yes", "No")),
      bsTooltip("set_all_features", "Create all features (ref/alt) or only those for the reference alleles?"),
      numericInput("set_indel_max_length", "Discard indels larger than this",
                   value=10),
      bsTooltip("set_indel_max_length", "Maximum length of indels to include (indels exceeding this size will be removed)."),
      radioButtons("set_indel_features", "Only create full-length features",
                   choices=c("Yes", "No"), selected="No"),
      bsTooltip("set_indel_features", "Only create full-length indel features or create additional features accounting for the size difference? See readme for a more in-depth explanation."),
      numericInput("set_barcodes_per_feature", "Barcodes added to each feature",
                   value=100),
      bsTooltip("set_barcodes_per_feature", "Number of barcodes to use per feature."),
      radioButtons("set_rev_comp", "Create reverse complementary versions of all features",
                   choices=c("Yes", "No"), selected="No"),
      bsTooltip("set_rev_comp", "Create reverse complementary versions of all features?"),
      textInput("enz_file_processed", "Enzyme file (processed)"),
      bsTooltip("enz_file_processed", "Path to processed enzyme file (columns: enzymes, site, expanded_sites). Expanded sites should be in a Python regex format, e.g. CTATCA[ACG]."),
      textInput("enz_file", "Enzyme file (NEB REBASE format)"),
      bsTooltip("enz_file", "Path to REBASE enzyme file (ignored if processed file used)."),
      textInput("enz_used", "All enzymes used"),
      bsTooltip("enz_used", "Enzymes used, comma-delimited (e.g. EcoRI,SbfI)."),
      textInput("enz_sites", "OR: all relevant cut sites (DOUBLE QUOTES)"),
      bsTooltip("enz_sites", "Expanded cut sites in a Python dictionary as Python regexes (e.g., ['GAATTC', 'CCTGCAGG'])."),
      numericInput("enz_cumul_cuts", "Total restriction sites expected",
                   value=2),
      bsTooltip("enz_cumul_cuts", "Total restriction sites expected in final feature, e.g. in the added sequences used for cloning."),
      numericInput("enz_cumul_cuts_bc", "Total restriction sites expected (in barcode plus the sequence before and after it)",
                   value=2),
      bsTooltip("enz_cumul_cuts_bc", "Total restriction sites expected in (barcode plus sequences right before and after it; used to screen the barcodes for excess restriction sites). Can be identical to total number of restriction sites expected."),
      radioButtons("out_format", "Output format",
                   choices=c(".json", ".tsv")),
      bsTooltip("out_format", "Output format, json or tab-separated."),
      textInput("out_output", "Output file path"),
      bsTooltip("out_output", "Path to designed output."),
      tags$hr(),
      tags$hr()
    )
  )
)

server <- function(input, output) {
  observeEvent(input$create_file, {
    #write("test = 'bla'\ntest2 = 'bla2'", "../z_testing.txt")
    in_vcf = ifelse(input$in_vcf == "", "None", paste0("'", input$in_vcf, "'"))
    in_sequence = ifelse(input$in_sequence == "", "None", paste0("'", input$in_sequence, "'"))
    in_barcode = paste0("'", input$in_barcode, "'")
    in_barcode_type = paste0("'", input$in_barcode_type, "'")
    db_genome = paste0("'", input$db_genome, "'")
    de_order = ifelse(input$de_order == "", paste0("'", "abcde", "'"), paste0("'", input$de_order, "'"))
    de_seq_1 = paste0("'", input$de_seq_1, "'")
    de_seq_2 = paste0("'", input$de_seq_2, "'")
    de_seq_3 = paste0("'", input$de_seq_3, "'")
    set_feature_size = input$set_feature_size
    set_all_features = ifelse(input$set_all_features == "Yes", 1, 0)
    set_indel_max_length = input$set_indel_max_length
    set_indel_features = ifelse(input$set_indel_features == "Yes", 1, 0)
    set_barcodes_per_feature = input$set_barcodes_per_feature
    set_rev_comp = ifelse(input$set_rev_comp == "Yes", 1, 0)
    enz_file_processed = ifelse(input$enz_file_processed == "", "None", paste0("'", input$enz_file_processed, "'"))
    enz_file = ifelse(input$enz_file == "", "None", paste0("'", input$enz_file, "'"))
    enz_used = ifelse(input$enz_used == "", "None", paste0("'", input$enz_used, "'"))
    enz_sites = ifelse(input$enz_sites == "", "None", paste0("'", input$enz_sites, "'"))
    enz_cumul_cuts = input$enz_cumul_cuts
    enz_cumul_cuts_bc = input$enz_cumul_cuts_bc
    out_format = paste0("'", input$out_format, "'")
    out_output = paste0("'", input$out_output, "'")
    
    final_output = paste0("in_vcf = ", in_vcf,
                          "\nin_sequence = ", in_sequence,
                          "\nin_barcode = ", in_barcode,
                          "\nin_barcode_type = ", in_barcode_type,
                          "\ndb_genome = ", db_genome,
                          "\nde_order = ", de_order,
                          "\nde_seq_1 = ", de_seq_1,
                          "\nde_seq_2 = ", de_seq_2,
                          "\nde_seq_3 = ", de_seq_3,
                          "\nset_feature_size = ", set_feature_size,
                          "\nset_all_features = ", set_all_features,
                          "\nset_indel_max_length = ", set_indel_max_length,
                          "\nset_indel_features = ", set_indel_features,
                          "\nset_barcodes_per_feature = ", set_barcodes_per_feature,
                          "\nset_rev_comp = ", set_rev_comp,
                          "\nenz_file_processed = ", enz_file_processed,
                          "\nenz_file = ", enz_file,
                          "\nenz_used = ", enz_used,
                          "\nenz_sites = ", enz_sites,
                          "\nenz_cumul_cuts = ", enz_cumul_cuts,
                          "\nenz_cumul_cuts_bc = ", enz_cumul_cuts_bc,
                          "\nout_format = ", out_format,
                          "\nout_output = ", out_output)
    write(final_output, "config_shiny.py")
  })
  
  output$download_file = downloadHandler(filename=function(){paste0("config_shiny.py")},
                                         content=function(filename){file.copy("config_shiny.py", filename)})
}

shinyApp(ui, server)