--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signac-add_gene_annotations.R	Tue Aug 02 19:11:27 2022 +0000
@@ -0,0 +1,70 @@
+#!/usr/bin/env Rscript
+
+# Load optparse we need to check inputs
+
+suppressPackageStartupMessages(require(optparse))
+
+# Load common functions
+
+suppressPackageStartupMessages(require(workflowscriptscommon))
+
+# parse options
+
+option_list = list(
+  make_option(
+    c("--signac-object"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Filtered peak BC matrix file in h5 format."
+  ),
+  make_option(
+    c("--ens-db-genome"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Metadata file."
+  ),
+  make_option(
+    c("--annotations"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Genome version."
+  ),
+  make_option(
+    c("--output-object-file"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "File name in which to store serialized R matrix object."
+  ) 
+)
+
+opt <- wsc_parse_args(option_list)
+
+suppressPackageStartupMessages(require(Seurat))
+suppressPackageStartupMessages(require(Signac))
+suppressPackageStartupMessages(require(GenomeInfoDb))
+suppressPackageStartupMessages(require(EnsDb.Hsapiens.v75))
+suppressPackageStartupMessages(require(EnsDb.Mmusculus.v79))
+
+set.seed(1234)
+
+# extract gene annotations from EnsDb
+signac_object <- readRDS(file = opt$signac_object)
+
+annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)
+print(annotations)
+
+# change to UCSC style since the data was mapped to hg19
+seqlevelsStyle(annotations) <- "UCSC"
+genome(annotations) <- opt$annotations
+
+# add the gene information to the object
+Annotation(signac_object) <- annotations
+
+print(signac_object)
+
+# Output to a serialized R object
+saveRDS(signac_object, file = opt$output_object_file)