spell check

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"),
@@ -43,33 +43,33 @@ 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)
 #' 
-#' @details If there is a header supplied other then the default data.table nameing scheme ('V1', 'V2', etc.) it will be kept and extended.
+#' @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) {
@@ -81,7 +81,7 @@ cdhitest <- function(input, identity = 0.8, coverage = 8, output = "cluster.bed"
   }
 
   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)
   } else {