Cluster

bin/cdhit_wrapper.R

@@ -4,7 +4,7 @@ library("optparse")
 option_list <- list(
   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("-A", "--coverage"), default = 8, help = "Minimal alignment length for both sequences in nucleotides. 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"),
@@ -14,15 +14,15 @@ option_list <- list(
   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_p"), default = 0.0, help = "Shorter sequences length must be at least x percent of longer sequences 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("-e", "--alignment_coverage_longer_p"), default = 0.0, help = "Alignment must cover x percent of longer sequence. Default = %default (CD-HIT parameter: -aL)", metavar = "double"),
   make_option(opt_str = c("-E", "--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: -AL)", metavar = "integer"),
   make_option(opt_str = c("-f", "--alignment_coverage_shorter_p"), default = 0.0, help = "Alignment must cover x percent of shorter sequence. Default = %default (CD-HIT parameter: -aS)", metavar = "double"),
   make_option(opt_str = c("-F", "--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: -AS)", metavar = "integer"),
   make_option(opt_str = c("-w", "--max_unmatched_longer_p"), default = 1.0, help = "Maximum unmatched percentage on longer sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter: -uL)", metavar = "double"),
   make_option(opt_str = c("-W", "--max_unmatched_shorter_p"), default = 1.0, help = "Maximum unmatched percentage on shorter sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter: -uS)", 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("-U", "--max_unmatched_both_n"), default = 99999999, help = "Maximum unmatched nucleotide 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"),
@@ -33,7 +33,8 @@ option_list <- list(
 )
 
 opt_parser <- OptionParser(option_list = option_list, 
-                           description = "CD-HIT-EST Wrapper function. See https://github.com/weizhongli/cdhit/wiki for more information regarding CD-HITs parameters.")
+                           description = "CD-HIT-EST Wrapper function. See https://github.com/weizhongli/cdhit/wiki for more information regarding CD-HITs parameters.",
+                           epilogue = "Author: Hendrik Schultheis <Hendrik.Schultheis@mpi-bn.mpg.de>")
 
 opt <- parse_args(opt_parser)
 
@@ -42,50 +43,59 @@ opt <- parse_args(opt_parser)
 #' 
 #' @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 coverage Minimal alignment length for both sequences in nucleotides. Default = 8 (CD-HIT parameter)
+#' @param output Clustered bed-file. 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_p Shorter sequences length must be at least x percent of longer sequences 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 max_unmatched_both_n Maximum unmatched nucleotide 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 gap_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)
 #' 
-#' TODO check whether cdhit is installed
+#' @details If there is a header supplied other then the default data.table naming scheme ('V1', 'V2', etc.) it will be kept and extended.
+#' 
 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 (system("which cd-hit-est", ignore.stdout = FALSE) != 0) {
+    stop("Required program CD-HIT not found! Please check whether it is installed.")
+  }
+
   if (missing(input)) {
-    stop("Input parameter missing!")
+    stop("No input specified! Please forward a valid bed-file.")
   }
 
   message("Loading bed.")
-  # load bed if neccessary
+  # load bed if necessary
   if (!data.table::is.data.table(input)) {
-    bed_table <- data.table::fread(input = input, header = FALSE)
+    bed_table <- data.table::fread(input = input)
   } else {
     bed_table <- input
   }
 
+  # check if there are column names to keep them
+  default_col_names <- grepl(pattern = "^V+\\d$", names(bed_table), perl = TRUE)
+  keep_col_names <- ifelse(any(default_col_names), FALSE, TRUE)
+
   # check for duplicated names
-  if (anyDuplicated(bed_table[, "V4"])) {
+  if (anyDuplicated(bed_table[, 4])) {
     warning("Found duplicated names. Making names unique.")
-    bed_table[, V4 := make.unique(V4)]
+    bed_table[, 4 := make.unique(names(bed_table)[4])]
   }
 
   message("Convert to fasta.")
@@ -137,17 +147,18 @@ cdhitest <- function(input, identity = 0.8, coverage = 8, output = "cluster.bed"
   system(command = cluster_call, wait = TRUE)
 
   # load reformated file
-  cluster <- data.table::fread(cluster_file)
+  cluster <- data.table::fread(cluster_file)[, c("id", "clstr")]
+  names(cluster) <- c("id", "cluster")
 
   ### add cluster to bed_table
-  result <- merge(x = bed_table, y = cluster[, c("id", "clstr")], by.x = "V4", by.y = "id", sort = FALSE)[, union(names(bed_table), names(cluster)[2]), with = FALSE]
+  result <- merge(x = bed_table, y = cluster, by.x = names(bed_table)[4], by.y = "id", sort = FALSE)[, union(names(bed_table), names(cluster)[2]), with = FALSE]
 
   # delete files
   if (clean) {
     file.remove(fasta_file, paste0(cdhit_output, ".clstr"), cdhit_output, cluster_file)
   }
 
-  data.table::fwrite(x = result, file = output, sep = "\t", col.names = FALSE)
+  data.table::fwrite(x = result, file = output, sep = "\t", col.names = keep_col_names)
 }
 
 # call function with given parameter if not in interactive context (e.g. run from shell)