--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/raceID_filter.R	Sat Mar 03 17:33:56 2018 -0500
@@ -0,0 +1,58 @@
+#!/usr/bin/env Rscript
+
+args = commandArgs(trailingOnly=T)
+
+script_dir = args[1]
+config_file = args[2]
+
+# Load libs, common functions, source RaceID and Galaxy Params
+source(paste(script_dir, "common.R", sep="/"))
+
+# Read input data
+x <- read.csv(count_matrix, sep="\t", header=TRUE)
+rownames(x) <- x[,1]
+
+message("Count matrix with %.0f cells and %.0f genes", dim(x)[1], dim(x)[2])
+
+# Control gene filtering
+# (if blank do nothing)
+if (!( (!exists("control_genes_filter")) || control_genes_filter == "" || control_genes_filter == "None")){
+    c_genes <- unlist(strsplit(control_genes_filter, "\\s*,\\s"))
+    for (cg in c_genes){
+        x <- x[grep(cg, rownames(x), invert=T), -1]
+        message("Filtering against %s yielded %.0f cells and %.0f genes", cg, dim(x)[1], dim(x)[2])
+    }
+} else {
+  x <- x[grep("INVALID", rownames(x), invert=T), -1]
+}
+
+if (!filtering){
+   # No filtering, just return an SCseq object
+   sc <- SCseq(x)
+   saveRDS(sc, output_rdat)
+   quit(status=0)
+}
+
+
+sc <- SCseq(x)
+
+if (c_maxexpr == 0){
+   c_maxexpr = Inf
+}
+
+# Perform actual filtering beyond this point
+message("Applying filtering parameters: mintotal = %.0f, minexpr = %.0f, minnumber= %.0f, maxexpr= %.0f, downsample= %.0f, dsn= %.0f, rseed=%.0f", c_mintotal, c_minexpr, c_minnumber, c_maxexpr, c_downsample, c_dsn, c_rseed)
+
+sc <- filterdata(sc,
+   mintotal=c_mintotal,
+   minexpr=c_minexpr,
+   minnumber=c_minnumber,
+   maxexpr=c_maxexpr, downsample = c_downsample, dsn=c_dsn, rseed=c_rseed)
+   
+message("Output matrix yielded %.0f cells and %.0f genes", dim(sc@fdata)[1], dim(sc@fdata)[2])
+
+# Output table
+write.table(sc@fdata, output_table, row.names = T, col.names = T, sep="\t", quote=F)
+# Output R object
+saveRDS(sc, output_rdat)
+