--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signac-geneactivity.R	Tue Aug 02 19:11:27 2022 +0000
@@ -0,0 +1,107 @@
+#!/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 = "A Seurat object."
+  ),
+  make_option(
+    c("--fragment-file"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Fragments file."
+  ),
+  make_option(
+    c("--assay"),
+    action = "store",
+    default = NULL,
+    type = 'character',
+    help = "Assay."
+  ),
+  make_option(
+    c("--features"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Features."
+  ),
+  make_option(
+    c("--extend-upstream"),
+    action = "store",
+    default = NA,
+    type = 'numeric',
+    help = "Number of bases to extend upstream of the TSS."
+  ),
+  make_option(
+    c("--extend-downstream"),
+    action = "store",
+    default = NA,
+    type = 'numeric',
+    help = "Number of bases to extend downstream of the TSS."
+  ),
+  make_option(
+    c("--biotypes"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Gene biotypes to include. If NULL, use all biotypes in the gene annotation."
+  ),
+  make_option(
+    c("--max-width"),
+    action = "store",
+    default = NA,
+    type = 'numeric',
+    help = "Maximum allowed gene width for a gene to be quantified."
+  ),
+  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))
+
+set.seed(1234)
+
+if (! file.exists(opt$signac_object)){
+  stop((paste('File', opt$signac_object, 'does not exist')))
+}
+
+signac_object <- readRDS(file = opt$signac_object)
+
+signac_object@assays$peaks@fragments[[1]]@path <- opt$fragment_file
+
+# Check features
+features <- NULL
+if (! is.null(opt$features) && opt$features != 'NULL'){
+  if (file.exists(opt$features)){
+    features <- readLines(opt$features)
+  }
+}
+
+# Check assay
+assay <- NULL
+if (! is.null(opt$assay) && opt$assay != 'NULL'){
+  assay <- opt$assay
+}
+
+saveRDS(GeneActivity(object = signac_object, assay = assay, features = features, extend.upstream = opt$extend_upstream, extend.downstream = opt$extend_downstream, biotypes = opt$biotypes, max.width = opt$max_width), file = opt$output_object_file)