#!/usr/bin/env Rscript
library(optparse)
description = "Remove chimeras and produce taxa table."
option_list = list(
make_option(c("-i", "--input"), type = "character", default = NULL,
help = "The file path for the sequence table in RDS format.",
metavar = "input_filepath"),
make_option(c("-o", "--output_dir"), type = "character", default = "./no_chim",
help = paste0("Directory where the no chimera sequence table ",
"file will be saved (default = ./no_chim)."),
metavar = "output_directory"),
make_option(c("-v", "--verbose"), default = FALSE, action = 'store_true',
help = "Print out extra info?")
)
opt_parser = OptionParser(option_list = option_list, description = description)
opt = parse_args(opt_parser)
if (is.null(opt$input)) {
print_help(opt_parser)
stop("No arguments supplied.\n", call. = FALSE)
}
seqtab = readRDS(opt$input)
seqtab.nochim = dada2::removeBimeraDenovo(seqtab, verbose = opt$verbose)
# print summary stats
message("ORIGINAL TABLE:\n")
message(paste0("Dimensions: ", paste(dim(seqtab), collapse = "; "), "\n"))
message("TABLE WITH CHIMERAS REMOVED:\n")
message(paste0("Dimensions: ", paste(dim(seqtab.nochim), collapse = "; "), "\n"))
message(paste0(
"Proportion seqs that were not chimeras: ",
sum(seqtab.nochim) / sum(seqtab),
"\n"
))
# output as r data objects
outdir = ifelse(
substr(opt$output_dir, nchar(opt$output_dir), nchar(opt$output_dir)) == '/',
opt$output_dir,
paste0(opt$output_dir, '/')
)
if (!dir.exists(outdir)) dir.create(outdir)
saveRDS(seqtab.nochim, file = paste0(outdir, "seqtab_nochim.RDS"))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.