MendelianVariants:

gatherGenes <- function(disease_file){
  gene_file <- data.frame(geneID = unique(unlist(strsplit(disease_file$genes, split = "; "))), stringsAsFactors = FALSE)
  gene_file$name <- character(dim(gene_file)[1])
  gene_file$ensembl_gene_id <- character(dim(gene_file)[1])
  gene_file$mim <- numeric(dim(gene_file)[1])
  gene_file$phenotype <- character(dim(gene_file)[1])


  split_gene <- strsplit(disease_file$genes, split = "; ")
  for(i in 1:length(split_gene)){
    for( j in 1:length(split_gene[[i]])){
      rownum <- which(gene_file$geneID == split_gene[i][[1]][j])
      if(gene_file$phenotype[rownum] !=""){
        gene_file$phenotype[rownum] <-
          paste(gene_file$phenotype[rownum],disease_file$title[i],sep = "; ")
      }
      else{
        gene_file$phenotype[rownum] <- disease_file$title[i]
      }
    }
  }
  gene_file <- gene_file[!gene_file$geneID == 0,]

  ####################
  # Entrez Gene Search
  ####################

  gene_file$summary <- entrez_summary(db="gene", id =gene_file$geneID)
  gene_file$name <- extract_from_esummary(gene_file$summary, "name")
  gene_file$description <- extract_from_esummary(gene_file$summary, "description")
  gene_file$chromosome <- extract_from_esummary(gene_file$summary, "chromosome")
  gene_file$map.location <- extract_from_esummary(gene_file$summary, "maplocation")
  gene_file$mim <- extract_from_esummary(gene_file$summary, "mim")
  gene_file$summary <- extract_from_esummary(gene_file$summary, "summary")

  ######################
  # Ensembl Gene Search
  ######################

  gene_file$start_position <- numeric(dim(gene_file)[1])
  gene_file$end_position <- numeric(dim(gene_file)[1])
  gene_file$strand <- numeric(dim(gene_file)[1])
  gene_file$cannonical_transcript <- character(dim(gene_file)[1])
  gene_file$exon <- character(dim(gene_file)[1])
  get_ensembl_info <- function(n){
    try({
      api.response <- fromJSON(paste("http://grch37.rest.ensembl.org/lookup/symbol/homo_sapiens/", gene_file$name[n],
                                     "?content-type=application/json;expand=1", sep = ""))
      gene_file$ensembl_gene_id[n] <<- api.response$id
      gene_file$start_position[n] <<- api.response$start
      gene_file$end_position[n] <<- api.response$end
      gene_file$strand[n] <<- api.response$strand
      transcripts <- as.data.frame(api.response)
      canonical.rownum <- which(transcripts$Transcript.is_canonical == 1)
      gene_file$cannonical_transcript[n] <<- transcripts$Transcript.id[canonical.rownum]
      gene_file$exon[n] <<- paste0(transcripts$Transcript.Exon[canonical.rownum][[1]]$start, " : ",
                                   transcripts$Transcript.Exon[canonical.rownum][[1]]$end, collapse = "; ")
    }, silent = TRUE)
  }
  sapply(1:dim(gene_file)[1], get_ensembl_info)
  gene_file$gnomAD.website <- sapply(1:dim(gene_file)[1], function(n){
    if(class(gene_file$ensembl_gene_id[[n]]) != "logical"){
      base_url <- "http://gnomad.broadinstitute.org/gene/"
      variantID <- gene_file$ensembl_gene_id[n]
      return(paste(base_url,variantID,sep = ""))
    }
    return(NULL)
  })
  gene_file$gnomAD.website <- lapply(gene_file$gnomAD.website, toString)
  gene_file$gnomAD.website <- unlist(gene_file$gnomAD.website)
  return(gene_file)
}







# gene_file <- genes
#   gene_file$hpa.url <- sapply(gene_file$ensembl_gene_id, function(x){
#     if(!is.logical(x)){
#       # if there is > 1 ensembl_gene_id, I am just using the first.
#       if(length(x) > 1){
#         paste("https://www.proteinatlas.org/",x[[1]],"/tissue/kidney", sep = "")
#       }
#       else{
#         paste("https://www.proteinatlas.org/",x,"/tissue/kidney", sep = "")
#       }
#     }
#   })
#
#
#
#   gene_file$page <- sapply(gene_file$hpa.url, function(x){
#     if(!is.null(x)){
#       tryCatch({read_html(x)},
#                error = function(e){
#                  return(NULL)
#                })
#     }
#   })
#   print(gene_file$hpa.page)
#
#   gene_file$hpa.rna.expression <- sapply(gene_file$page, function(x){
#     if(!is.null(x)){
#       print(x)
#       x %>% html_nodes("body table.main_table tr div.menu_margin table.border.dark.round table.noborder.nowrap tr"
#       )}})
#
#   print(gene_file$hpa.rna.expression)
#   gene_file$hpa.rna.hpa.tpm <- sapply(gene_file$hpa.rna.expression, function(x){
#     if(!is.null(x)){
#       as.list(x[1] %>% html_nodes("td") %>% html_text())[[2]]}})
#   gene_file$hpa.rna.hpa.tpm <- lapply(gene_file$hpa.rna.hpa.tpm, toString)
#   gene_file$hpa.rna.hpa.tpm <- unlist(gene_file$hpa.rna.hpa.tpm)
#
#   gene_file$hpa.rna.gtex.rpkm <- sapply(gene_file$hpa.rna.expression, function(x){
#     if(!is.null(x)){
#       tryCatch({as.list(x[2] %>% html_nodes("td") %>% html_text())[[2]]},
#                error = function(e){
#                  return(NULL)
#                })}})
#   gene_file$hpa.rna.gtex.rpkm <- lapply(gene_file$hpa.rna.gtex.rpkm, toString)
#   gene_file$hpa.rna.gtex.rpkm <- unlist(gene_file$hpa.rna.gtex.rpkm)
#
#   gene_file$hpa.rna.fantom5.tagspermillion <- sapply(gene_file$hpa.rna.expression, function(x){
#     if(!is.null(x)){
#       tryCatch({as.list(x[3] %>% html_nodes("td") %>% html_text())[[2]]},
#                error = function(e){
#                  return(NULL)
#                })}})
#   gene_file$hpa.rna.fantom5.tagspermillion <- lapply(gene_file$hpa.rna.fantom5.tagspermillion, toString)
#   gene_file$hpa.rna.fantom5.tagspermillion <- unlist(gene_file$hpa.rna.fantom5.tagspermillion)
#
#   gene_file$hpa.protein.expression <- sapply(gene_file$page, function(x){
#     if(!is.null(x)){
#       x %>% html_nodes("body table.main_table tr div.menu_margin table table.dark th.nopadd table.border.dark table.noborder.nowrap tr")
#     }})
#
#   gene_file$hpa.protein.glomeruli <- sapply(gene_file$hpa.protein.expression, function(x){
#     if(!is.null(x)){
#       tryCatch({as.list(x[1] %>% html_nodes("td") %>% html_text)[[2]]},
#                error = function(e){
#                  return(NULL)
#                })}})
#   gene_file$hpa.protein.glomeruli <- lapply(gene_file$hpa.protein.glomeruli, toString)
#   gene_file$hpa.protein.glomeruli <- unlist(gene_file$hpa.protein.glomeruli)
#
#   gene_file$hpa.protein.tubules <- sapply(gene_file$hpa.protein.expression, function(x){
#     if(!is.null(x)){
#       tryCatch({as.list(x[2] %>% html_nodes("td") %>% html_text)[[2]]},
#                error = function(e){
#                  return(NULL)
#                })}})
#   gene_file$hpa.protein.tubules <- lapply(gene_file$hpa.protein.tubules, toString)
#   gene_file$hpa.protein.tubules <- unlist(gene_file$hpa.protein.tubules)
#   gene_file <- gene_file[ , !(names(gene_file) %in% c("page", "hpa.rna.expression",
#                                                       "hpa.protein.expression"))]
#
#