--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_from_dada2.R	Thu Mar 03 13:28:30 2022 +0000
@@ -0,0 +1,39 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("phyloseq"))
+suppressPackageStartupMessages(library("tidyverse"))
+
+option_list <- list(
+    make_option(c("--sequence_table"), action = "store", dest = "sequence_table", help = "Input sequence table"),
+    make_option(c("--taxonomy_table"), action = "store", dest = "taxonomy_table", help = "Input taxonomy table"),
+    make_option(c("--output"), action = "store", dest = "output", help = "RDS output")
+)
+
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list);
+args <- parse_args(parser, positional_arguments = TRUE);
+opt <- args$options;
+
+# The input sequence_table is an integer matrix
+# stored as tabular (rows = samples, columns = ASVs).
+seq_table_numeric_matrix <- data.matrix(read.table(opt$sequence_table, sep = "\t"));
+
+# The input taxonomy_table is a table containing
+# the assigned taxonomies exceeding the minBoot
+# level of bootstrapping confidence. Rows correspond
+# to sequences, columns to taxonomic levels. NA
+# indicates that the sequence was not consistently
+# classified at that level at the minBoot threshold.
+tax_table_matrix <- as.matrix(read.table(opt$taxonomy_table, header = FALSE, sep = "\t"));
+
+# Construct a tax_table object.  The rownames of
+# tax_tab must match the OTU names (taxa_names)
+# of the otu_table defined below.
+tax_tab <- tax_table(tax_table_matrix);
+
+# Construct an otu_table object.
+otu_tab <- otu_table(seq_table_numeric_matrix, taxa_are_rows = TRUE);
+
+# Construct a phyloseq object.
+phyloseq_obj <- phyloseq(otu_tab, tax_tab);
+saveRDS(phyloseq_obj, file = opt$output, compress = TRUE);