## summarize hits
output = commandArgs(T)[2] ## output table
filepath = commandArgs(T)[1]  ## input dante gff3
summarized_by = commandArgs(T)[-(1:2)]

readGFF3fromDante = function(filepath){
  dfraw=read.table(filepath, as.is = TRUE)
  gff_df = dfraw[,1:8]
  colnames(gff_df) = c("seqid", "source", "type", "start", "end", "score",
                    "strand", "phase")
  ## assume same order, same attributes names
  gffattr = do.call(rbind,
                    lapply(
                      strsplit(dfraw[,9],split=c("=|;")),
                      function(x)x[c(FALSE,TRUE)]
                    )
                    )
  gff_df$Name = gffattr[,1]
  gff_df$Final_Classification = gffattr[,2]
  gff_df$Region_Hits_Classifications = gffattr[,3]
  gff_df$Best_Hit = gffattr[,4]
  gff_df$Best_Hit_DB_Pos = gffattr[,5]
  gff_df$DB_Seq = gffattr[,6]
  gff_df$Query_Seq = gffattr[,7]
  gff_df$Identity = as.numeric(gffattr[,8])
  gff_df$Similarity = as.numeric(gffattr[,9])
  gff_df$Relat_Length = as.numeric(gffattr[,10])
  gff_df$Relat_Interruptions = as.numeric(gffattr[,11])
  gff_df$Hit_to_DB_Length = as.numeric(gffattr[,12])
  return(gff_df)
}

gff = readGFF3fromDante(filepath)
# summarize_by = c("Final_Classification", "Name", "seqid")

tbl = data.frame(table(gff[,summarize_by]))
write.table(tbl, file = filepath, row.names =FALSE, quote = FALSE)