Cluster

bin/cdhit_wrapper.R

@@ -2,50 +2,133 @@
 library("optparse")
 
 option_list <- list(
-  make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file. Last column must be sequences.", metavar = "character"),
-  make_option(opt_str = c("-s", "--similarity"), default = 0.8, help = "Similarity threshold. Default = %default", metavar = "double >= 0.8"),
-  make_option(opt_str = c("-A", "--coverage"), default = 8, help = "Minimal alignment length for both sequences in nucelotides. Default = %default", metavar = "integer"),
-  make_option(opt_str = c("-o", "--output"), default = "cluster.bed", help = "Output file. Default = %default", metavar = "character"),
-  make_option(opt_str = c("-c", "--clean"), default = TRUE, help = "Delete all temporary files. Default = %default", metavar = "logical")
-  # TODO more args
+  make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file. Fourth column is expected to contain names, last column must be sequences.", metavar = "character"),
+  make_option(opt_str = c("-c", "--identity"), default = 0.8, help = "Identity threshold. Default = %default (CD-HIT parameter)", metavar = "double >= 0.8"),
+  make_option(opt_str = c("-A", "--coverage"), default = 8, help = "Minimal alignment length for both sequences in nucelotides. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-o", "--output"), default = "cluster.bed", help = "Output file same as input but with appended column of cluster numbers. Default = %default", metavar = "character"),
+  make_option(opt_str = c("--clean"), default = TRUE, help = "Delete all temporary files. Default = %default", metavar = "logical"),
+  make_option(opt_str = c("-G", "--global"), default = 0, help = "Global sequence identity = 1, local = 0. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-b", "--band_width"), default = 20, help = "Alignment band width. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-M", "--memory"), default = 800, help = "Memory limit in MB. 0 for unlimited. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-T", "--threads"), default = 1, help = "Number of threads. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-n", "--word_length"), default = 3, help = "Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-l", "--throw_away_sequences"), default = 5, help = "Maximum length of sequences thrown away. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  # make_option(opt_str = c("-d", "--description")), # can not produce bed if this is != 0
+  make_option(opt_str = c("-s", "--length_dif_cutoff_shorter_p"), default = 0.0, help = "Shorter sequences length must be at least x percent of longer sequenecs length. Default = %default (CD-HIT parameter)", metavar = "double"),
+  make_option(opt_str = c("-S", "--length_dif_cutoff_shorter_n"), default = 999999, help = "Length difference between sequences can not be higher than x nucleotides. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-aL", "--alignment_coverage_longer_p"), default = 0.0, help = "Alignment must cover x percent of longer sequence. Default = %default (CD-HIT parameter)", metavar = "double"),
+  make_option(opt_str = c("-AL", "--alignment_coverage_longer_n"), default = 99999999, help = "There can not be more than x unaligned nucleotides on the longer sequence. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-aS", "--alignment_coverage_shorter_p"), default = 0.0, help = "Alignment must cover x percent of shorter sequence. Default = %default (CD-HIT parameter)", metavar = "double"),
+  make_option(opt_str = c("-AS", "--alignment_coverage_shorter_n"), default = 99999999, help = "There can not be more than x unaligned nucleotides on the longer sequence. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-uL", "--max_unmatched_longer_p"), default = 1.0, help = "Maximum unmatched percentage on longer sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter)", metavar = "double"),
+  make_option(opt_str = c("-uS", "--max_unmatched_shorter_p"), default = 1.0, help = "Maximum unmatched percentage on shorter sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter)", metavar = "double"),
+  make_option(opt_str = c("-U", "--max_unmatched_both_n"), default = 99999999, help = "Maximum unmatched nucleotied on both sequences (excludes leading tailing gap). Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-g", "--fast_cluster"), default = 1, help = "Cluster sequence in first cluster that meets threshold = 0 (fast). Or cluster in best Cluster = 1 (accurate). Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-r", "--strand"), default = 0, help = "Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("--match"), default = 2, help = "Matching score. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("--mismatch"), default = -2, help = "Mismatch score. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("--gap"), default = -6, help = "Gap score. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("--gap_ext"), default = -1, help = "Gap extension score. Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-sc", "--sort_cluster_by_size"), default = 1, help = "Either sort cluster by decreasing length (= 0) or by decreasing size (= 1). Default = %default (CD-HIT parameter)", metavar = "integer")
 )
 
 opt_parser <- OptionParser(option_list = option_list, 
-                           description = "CD-HIT-EST Wrapper function.")
+                           description = "CD-HIT-EST Wrapper function. See https://github.com/weizhongli/cdhit/wiki for more information regarding CD-HITs parameters.")
 
 opt <- parse_args(opt_parser)
 
-#' cd-hit wrapper
+#' cd-hit-est wrapper
+#' Receives bed with sequences in last column and writes bed with added cluster numbers.
 #' 
-#' @param input
-#' @param similarity Similarity threshold.
-#' @param coverage Minimal alignment length for both sequences in nucelotides.
-#' @param output Clustered bedfile. Adds cluster number in last column (lower number = bigger cluster).
-#' @param clean Clean up after run.
+#' @param input Data.table or file in bed format (requires names in fourth column and sequences in last column).
+#' @param identity Identity threshold. Default = 0.8 (CD-HIT parameter)
+#' @param coverage Minimal alignment length for both sequences in nucelotides. Default = 8 (CD-HIT parameter)
+#' @param output Clustered bedfile. Adds cluster number in last column (numbering depend on sort_by_cluster_size parameter). Default = cluster.bed
+#' @param clean Clean up after run. Default = TRUE
+#' @param threads Number of threads to use (0 = all cores). Default = 1 (CD-HIT parameter)
+#' @param global Global sequence identity = 1, local = 0. Default = 0 (CD-HIT parameter)
+#' @param band_width "Alignment band width. Default = 20 (CD-HIT parameter)"
+#' @param memory Memory limit in MB. 0 for unlimited. Default = 800 (CD-HIT parameter)
+#' @param word_length Default = 3 (CD-HIT parameter)
+#' @param throw_away_sequences Maximum length of sequences thrown away. Default = %default (CD-HIT parameter)
+#' @param length_dif_cutoff_shorter_p Shorter sequences length must be at least x percent of longer sequenecs length. Default = 0 (CD-HIT parameter)
+#' @param length_dif_cutoff_shorter_n Length difference between sequences can not be higher than x nucleotides. Default = 999999 (CD-HIT parameter)
+#' @param alignment_coverage_longer_p Alignment must cover x percent of longer sequence. Default = 0 (CD-HIT parameter)
+#' @param alignment_coverage_longer_n There can not be more than x unaligned nucleotides on the longer sequence. Default = 99999999 (CD-HIT parameter)
+#' @param alignment_coverage_shorter_p Alignment must cover x percent of shorter sequence. Default = 0 (CD-HIT parameter)
+#' @param alignment_coverage_shorter_n There can not be more than x unaligned nucleotides on the longer sequence. Default = 99999999 (CD-HIT parameter)
+#' @param max_unmatched_longer_p Maximum unmatched percentage on longer sequence (excludes leading tailing gap). Default = 1 (CD-HIT parameter)
+#' @param max_unmatched_shorter_p Maximum unmatched percentage on shorter sequence (excludes leading tailing gap). Default = 1 (CD-HIT parameter)
+#' @param max_unmatched_both_n Maximum unmatched nucleotied on both sequences (excludes leading tailing gap). Default = 99999999 (CD-HIT parameter)
+#' @param fast_cluster Cluster sequence in first cluster that meets threshold = 0 (fast). Or cluster in best Cluster = 1 (accurate). Default = 1 (CD-HIT parameter)
+#' @param strand Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = 0 (CD-HIT parameter)
+#' @param match Matching score. Default = 2 (CD-HIT parameter)
+#' @param mismatch Mismatch score. Default = -2 (CD-HIT parameter)
+#' @param gap Gap score. Default = -6 (CD-HIT parameter)
+#' @param gat_ext Gap extension score. Default = -1 (CD-HIT parameter)
+#' @param sort_cluster_by_size Either sort cluster by decreasing length (= 0) or by decreasing size (= 1). Default = 1 (CD-HIT parameter)
 #' 
-#' @return bed_table with cluster in last column
-#' TODO add all cdhit parameter
 #' TODO check whether cdhit is installed
-cdhitest <- function(input, similarity = 0.8, coverage = 8, output = "cluster.bed", clean = TRUE) {
+cdhitest <- function(input, identity = 0.8, coverage = 8, output = "cluster.bed", clean = TRUE, threads = 1, global = 0, band_width = 20, memory = 800, word_length = 3, throw_away_sequences = 5, length_dif_cutoff_shorter_p = 0, length_dif_cutoff_shorter_n = 999999, alignment_coverage_longer_p = 0, alignment_coverage_longer_n = 99999999, alignment_coverage_shorter_p = 0, alignment_coverage_shorter_n = 99999999, max_unmatched_longer_p = 1, max_unmatched_shorter_p = 1, max_unmatched_both_n = 99999999, fast_cluster = 1, strand = 0, match = 2, mismatch = -2, gap = -6, gap_ext = -1, sort_cluster_by_size = 1) {
+  if (missing(input)) {
+    stop("Input parameter missing!")
+  }
+
+  message("Loading bed.")
   # load bed if neccessary
   if (!data.table::is.data.table(input)) {
     bed_table <- data.table::fread(input = input, header = FALSE)
   } else {
     bed_table <- input
   }
 
+  # check for duplicated names
+  if (anyDuplicated(bed_table[, "V4"])) {
+    warning("Found duplicated names. Making names unique.")
+    bed_table[, V4 := make.unique(V4)]
+  }
+
+  message("Convert to fasta.")
   ### convert bed to fasta
   # 4th column = name
   # last column = sequence
   fasta_file <- "converted_bed.fasta"
   seqinr::write.fasta(sequences = as.list(bed_table[[ncol(bed_table)]]), names = bed_table[[4]], as.string = TRUE, file.out = fasta_file)
 
+  message("Clustering.")
   ### cd-hit-est
   cdhit_output <- "cdhit_output"
-  cdhit_call <- paste("cd-hit-est -i", fasta_file, "-o", cdhit_output, "-c", similarity, "-A", coverage, "-G 0 -n 3 -g 1 -r 0 -l 5 -sc 1 -d 0")
+  cdhit_call <- paste("cd-hit-est -i", fasta_file,
+                      "-o", cdhit_output,
+                      "-c", identity,
+                      "-A", coverage,
+                      "-T", threads,
+                      "-G", global,
+                      "-b", band_width,
+                      "-M", memory,
+                      "-n", word_length,
+                      "-l", throw_away_sequences,
+                      "-s", length_dif_cutoff_shorter_p,
+                      "-S", length_dif_cutoff_shorter_n,
+                      "-aL", alignment_coverage_longer_p,
+                      "-AL", alignment_coverage_longer_n,
+                      "-aS", alignment_coverage_shorter_p,
+                      "-AS", alignment_coverage_shorter_n,
+                      "-uL", max_unmatched_longer_p,
+                      "-uS", max_unmatched_shorter_p,
+                      "-U", max_unmatched_both_n,
+                      "-g", fast_cluster,
+                      "-r", strand,
+                      "-match", match,
+                      "-mismatch", mismatch,
+                      "-gap", gap,
+                      "-gap-ext", gap_ext,
+                      "-sc", sort_cluster_by_size,
+                      "-d 0")
 
   system(command = cdhit_call, wait = TRUE)
 
+  message("Formatting/ writing results.")
   # reformat cluster file
   # columns: id, clstr, clstr_size, length, clstr_rep, clstr_iden, clstr_cov
   cluster_file <- "reformated.clstr"
@@ -71,5 +154,5 @@ cdhitest <- function(input, similarity = 0.8, coverage = 8, output = "cluster.be
 if (!interactive()) {
   # remove last parameter (help param)
   params <- opt[-length(opt)]
-  do.call(cdhitest, args = params)  
+  do.call(cdhitest, args = params)
 }