From c6c42ca1e19e6a3f838a3960cd732e86ae96ff21 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Thu, 6 Dec 2018 12:30:21 +0100 Subject: [PATCH] renamed ignore_strand to strand --- bin/cdhit_wrapper.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/bin/cdhit_wrapper.R b/bin/cdhit_wrapper.R index 9c62564..c9a8241 100644 --- a/bin/cdhit_wrapper.R +++ b/bin/cdhit_wrapper.R @@ -24,7 +24,7 @@ option_list <- list( 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", "--ignore_strand"), default = 0, help = "Align +/+ & +/- (= 1). Or align only +/+ (= 0). 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"), @@ -61,7 +61,7 @@ opt <- parse_args(opt_parser) #' @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 ignore_strand Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = 0 (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) @@ -69,7 +69,7 @@ opt <- parse_args(opt_parser) #' @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 -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, ignore_strand = 0, match = 2, mismatch = -2, gap = -6, gap_ext = -1, sort_cluster_by_size = 1) { +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!") } @@ -118,7 +118,7 @@ cdhitest <- function(input, identity = 0.8, coverage = 8, output = "cluster.bed" "-uS", max_unmatched_shorter_p, "-U", max_unmatched_both_n, "-g", fast_cluster, - "-r", ignore_strand, + "-r", strand, "-match", match, "-mismatch", mismatch, "-gap", gap,