1 files changed, 39 insertions, 0 deletions
diff --git a/src/filter_max_bg_mers.py b/src/filter_max_bg_mers.py
new file mode 100755
index 0000000..8ea38a4
--- /dev/null
+++ b/src/filter_max_bg_mers.py
@@ -0,0 +1,39 @@
+#!/usr/bin/env python2.7
+import sys, os
+	
+def main():
+
+	if(len(sys.argv) < 2):
+		print "cutoff and bg_counts is expected as an argument"
+		exit()
+	else:
+		cutoff = int(sys.argv[1])
+		bg_count_fn = sys.argv[2]
+	
+	# if  cutoff, is less than zero, we ignore, aka so we can do -1 by default,
+	# we can't do 0, because that might have a valid use case
+	if cutoff < 0:
+		for line in sys.stdin:
+			sys.stdout.write(line)
+	else:
+
+		mers = {}
+
+		bg_count_fh = open(bg_count_fn, "r")
+		
+		# copy in our foreground mers and counts into mers dictionary, then process it
+		for line in sys.stdin:
+			(mer, count) = line.split()
+			mers[mer] = [int(count), -1]
+		
+		for line in bg_count_fh:
+			(mer, count) = line.split()
+			if mer in mers:
+				mers[mer][1] = int(count)
+
+		for mer in mers:
+			if mers[mer][1] == -1 or mers[mer][1] <= cutoff:
+				sys.stdout.write(mer + '\t' + str(mers[mer][0]) + '\n')
+
+if __name__ == "__main__":
+	sys.exit(main())