From d4ec5459d0fc141d20a4bbbf0a7dc40742e0372f Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Wed, 13 Aug 2014 16:59:37 -0400
Subject: add filter max bg mers

---
 SelectiveWholeGenomeAmplification | 10 +++++++++-
 src/filter_max_bg_mers.py         | 39 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+), 1 deletion(-)
 create mode 100755 src/filter_max_bg_mers.py

diff --git a/SelectiveWholeGenomeAmplification b/SelectiveWholeGenomeAmplification
index 7a3d46b..8304387 100755
--- a/SelectiveWholeGenomeAmplification
+++ b/SelectiveWholeGenomeAmplification
@@ -182,6 +182,9 @@ done
 # bg_ratio
 : ${min_bg_ratio=0}
 
+# max_bg_mers
+: ${max_bg_mers=-1}
+
 export ignore_mers
 export min_mer_range
 export max_mer_range
@@ -246,6 +249,7 @@ ignore_all_mers_counts="$output_directory/$current_run/passes-filter/2-$fg_basen
 average_binding="$output_directory/$current_run/passes-filter/3-$fg_basename-average-binding"
 non_melting="$output_directory/$current_run/passes-filter/4-$fg_basename-non-melting"
 consecutive_binding="$output_directory/$current_run/passes-filter/5-$fg_basename-consecutive-binding"
+bg_filtered="$output_directory/$current_run/passes-filter/6-$fg_basename-bg-filtered"
 
 # Make our output directory
 if [[ ! -d "$output_directory" ]]; then
@@ -342,7 +346,11 @@ if [[ -n "$step_filters" ]] || [[ -n "$all" ]]; then
 	filter_max_consecutive_binding.py "$max_consecutive_binding" < "$non_melting" > "$consecutive_binding" || exit 1
 	check_non_empty "$consecutive_binding" "consecutive binding"
 
-	cp $consecutive_binding $final_fg_counts
+	echo "  filtering mers that have more bg mers than allowed ($max_bg_mers)"
+	filter_max_bg_mers.py "$max_bg_mers" "$bg_counts" < "$consecutive_binding" > "$bg_filtered" || exit 1
+	check_non_empty "$bg_filtered" "background filtered"
+
+	cp $bg_filtered $final_fg_counts
 fi
 
 if [[ -n "$step_select" ]] || [[ -n "$all" ]]; then
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())
-- 
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