R/db_exploring.R

In bbica/MetaViral:

#' @title db_exploring
#' @description isolates the database selected, counts for the biome and can perform other manipulations
#' #'
#' @param viral_annotations dataframe from DRAMv
#' @param database database to further analize
#' @import dplyr
#' @import tidyr
#' @import KEGGREST
#' @examples
#' \dontrun{
#' quiet(cat("test"))
#' quiet(warning("test"))
#' quiet(warning("test"), all=T)
#' }
#' # This is a function that suppresses log info
#' @export
db_exploring<-function(viral_annotations, database="all"){
  '%>%' <- tidyr::`%>%`
  if (database=="peptidase"){
    peptidase<-dplyr::select(viral_annotations, peptidase_hit, peptidase_id, peptidase_family, peptidase_RBH, peptidase_eVal, Biome, fasta)
    peptidase<-na.omit(peptidase)
    peptidase<-peptidase %>%
      dplyr::add_count(peptidase_hit,name="peptidase_counts", Biome)
    return(peptidase)

  }else if (database=="vog"){
    vog<-dplyr::select(viral_annotations, vogdb_description, Biome, fasta)
    vog<-na.omit(vog)
    vog<-vog %>%
      dplyr::add_count(vogdb_description,name="vog_counts", Biome)
    return(vog)

  }else if (database=="kegg"){

    kegg<-dplyr::select(viral_annotations, Biome, kegg_hit, kegg_id, fasta)
    kegg<-tidyr::separate_rows(kegg, kegg_id , sep = ",", convert = FALSE)
    kegg<-unique(kegg[, c( "Biome", "kegg_hit", "kegg_id", "fasta")])
    kegg<-na.omit(kegg)
    kegg<-kegg %>%
      dplyr::add_count(kegg_hit,name="kegg_counts", Biome)
    kegg<-unique(kegg[, c("Biome","kegg_hit","kegg_id","kegg_counts","fasta")])
    kegg$Pathway<-NA
    kegg$Pathway2<-NA
    kegg$Pathway3<-NA

    for (i in 1:nrow(kegg)) {
      protein_id<-c(kegg$kegg_id[i])
      query<-tryCatch(KEGGREST::keggGet(protein_id), error=function(e) NULL)

      if (length(query[[1]]$PATHWAY)==1) {
        kegg$Pathway[i]<-query[[1]]$PATHWAY

      } else if (length(query[[1]]$PATHWAY)==2) {
        kegg$Pathway[i]<-query[[1]]$PATHWAY[1]
        kegg$Pathway2[i]<-query[[1]]$PATHWAY[2]

      } else if (length(query[[1]]$PATHWAY)==3) {
        kegg$Pathway[i]<-query[[1]]$PATHWAY[1]
        kegg$Pathway2[i]<-query[[1]]$PATHWAY[2]
        kegg$Pathway3[i]<-query[[1]]$PATHWAY[3]
      }
    }#end of for loop

    kegg<-kegg %>%
      dplyr::add_count(Pathway,name="pathway_counts", Biome)

    return(kegg)

  }else if (database=="pfam"){
    pfam<-dplyr::select(viral_annotations, Biome, pfam_hits, pfam_id, fasta)
  pfam<-na.omit(pfam)
  pfam<-pfam %>%
    dplyr::add_count(pfam_hits,name="pfam_counts", Biome)
  return(pfam)

  }else if (database=="refseq"){
    refseq<-dplyr::select(viral_annotations, Biome, viral_function, viral_id, viral_tax, viral_identity,
    viral_bitScore, viral_eVal, fasta)
  refseq<-na.omit(refseq)
  refseq<-refseq %>%
    dplyr::add_count(viral_function,name="viral_counts", Biome)
  return(refseq)

  }else if (database=="cazy"){ #dbCAN, automated carbohydrate-active enzyme (CAZyme) annotation (http://bcb.unl.edu/dbCAN2/)
    cazy<-dplyr::select(viral_annotations, Biome, cazy_hits, fasta)
    cazy<-na.omit(cazy)
    cazy<- cazy %>%
      dplyr::add_count(cazy_hits, name="cazy_counts", Biome)
    return(cazy)

  }else if (database=="all"){
    peptidase<-dplyr::select(viral_annotations, peptidase_hit, peptidase_id, peptidase_family, peptidase_RBH, peptidase_eVal, Biome)
    peptidase<-na.omit(peptidase)
    peptidase<-peptidase %>%
      dplyr::add_count(peptidase_hit,name="peptidase_counts", Biome)%>%
      unique(peptidase[, c("peptidase_hit","Biome","peptidase_counts", "fasta")])


    vog<-dplyr::select(viral_annotations, vogdb_description, Biome)
    vog<-na.omit(vog)
    vog<-vog %>%
      dplyr::add_count(vogdb_description,name="vog_counts", Biome)%>%
      unique(vog[, c("vogdb_description","Biome","vog_counts", "fasta")])

    kegg<-dplyr::select(viral_annotations, Biome, kegg_hit, kegg_id)
    kegg<-na.omit(kegg)
    kegg<-kegg %>%
      dplyr::add_count(kegg_hit,name="kegg_counts", Biome)%>%
      unique(kegg[, c("kegg_hit","kegg_id","Biome","kegg_counts", "fasta")])

    kegg$Pathway<-NA
    kegg$Pathway2<-NA
    kegg$Pathway3<-NA

    for (i in 1:nrow(kegg)) {
      protein_id<-c(kegg$kegg_id[i])
      query<-tryCatch(KEGGREST::keggGet(protein_id), error=function(e) NULL)

      if (length(query[[1]]$PATHWAY)==1) {
        kegg$Pathway[i]<-query[[1]]$PATHWAY

      } else if (length(query[[1]]$PATHWAY)==2) {
        kegg$Pathway[i]<-query[[1]]$PATHWAY[1]
        kegg$Pathway2[i]<-query[[1]]$PATHWAY[2]

      } else if (length(query[[1]]$PATHWAY)==3) {
        kegg$Pathway[i]<-query[[1]]$PATHWAY[1]
        kegg$Pathway2[i]<-query[[1]]$PATHWAY[2]
        kegg$Pathway3[i]<-query[[1]]$PATHWAY[3]
      }
    }#end of for loop

    kegg<-kegg %>%
      dplyr::add_count(Pathway,name="pathway_counts", Biome)

    pfam<-dplyr::select(viral_annotations, Biome, pfam_hits, pfam_id)
    pfam<-na.omit(pfam)
    pfam<-pfam %>%
      dplyr::add_count(pfam_hits,name="pfam_counts", Biome)%>%
      unique(pfam[, c("pfam_hits","Biome","pfam_counts")])


    refseq<-dplyr::select(viral_annotations, Biome, viral_function, viral_id, viral_tax, viral_identity,
                           viral_bitScore, viral_eVal)
    refseq<-na.omit(refseq)
    refseq<-refseq %>%
      dplyr::add_count(viral_function,name="viral_counts", Biome)%>%
      unique(refseq[, c("viral_function","Biome","viral_counts")])

    cazy<-dplyr::select(viral_annotations, Biome, cazy_hits)
    cazy<-na.omit(cazy)
    cazy<- cazy %>%
      dplyr::add_count(cazy_hits, name="cazy_counts", Biome)%>%
      unique(cazy[, c("cazy_hits","Biome","cazy_counts")])

    #merge all db
    database_all<-Reduce(function(x,y) merge(x,y,by="Biome",all=TRUE) ,list(kegg, pfam, vog, refseq, peptidase, cazy))
    return(database_all)

  }else {
    warning("choose one of the following: kegg, pfam, vog, refseq, cazy, peptidase or all")
  }
}#end of function