R/split_clstr_file.R

In jfq3/RDPutils: R Utilities for Processing RDPTool Output

split_clstr_file <-
function(clstr_file="all_seq_complete.clust", file.prefix="dist_") {
  # Read in cluster file.
  clust <- read.delim(file=clstr_file, header=FALSE, as.is=TRUE)
  cluster.header <- clust[1:2, ] # Keep first 2 lines to print with subsetted cluster file.
  
  # Make index of row numbers for each distance in cluster file.
  line.no <- which(clust[ , 1]=="distance cutoff:")
  distance <- clust[line.no, 2]
  dist.index <- data.frame(line.no, distance)  
  
  # Get first and last row numbers for chosen distance.
 for (n in 1:nrow(dist.index)) {
    if (n==nrow(dist.index)) {
      first.row <- as.numeric(dist.index[n,1])
      last.row <- nrow(clust)
    } else {
      first.row <- as.numeric(dist.index[n,1])
      last.row <- as.numeric(dist.index[n+1,1])-1
    }
    # Subset lines in cluster file to chosen distance
    clus <- clust[first.row:last.row, ]
    # Write file
    file.name <- paste(file.prefix,as.character(dist.index[n,2]),".clust", sep="")
    cluster <- rbind(cluster.header, clus)
    write.table(cluster, file=file.name, sep="\t", col.names=FALSE, row.names=FALSE)
  }
message <- paste("Wrote ",nrow(dist.index), " cluster files to disk.", sep="")
return(message)
}