From 428cc8fc9c27de8a24e6bcfc426a11e7839cebbd Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Fri, 22 Aug 2014 17:37:49 -0400
Subject: revamp filter_average_binding.py

---
 SelectiveWholeGenomeAmplification |  2 +-
 src/filter_average_binding.py     | 55 +++++++++++++++++++++++++++++----------
 2 files changed, 42 insertions(+), 15 deletions(-)

diff --git a/SelectiveWholeGenomeAmplification b/SelectiveWholeGenomeAmplification
index 8304387..b2b95ca 100755
--- a/SelectiveWholeGenomeAmplification
+++ b/SelectiveWholeGenomeAmplification
@@ -335,7 +335,7 @@ if [[ -n "$step_filters" ]] || [[ -n "$all" ]]; then
 	check_non_empty "$ignore_all_mers_counts" "ignore all mers from file "
 	
 	echo "  filtering mers that appear less frequently than the average binding site distance ($min_foreground_binding_average)"
-	filter_average_binding.py "$ignore_all_mers_counts" "$min_foreground_binding_average" < "$fg_counts"  > "$average_binding" || exit 1
+	filter_average_binding.py --fasta "$foreground" --minimum "$min_foreground_binding_average" --counts "$ignore_all_mers_counts"  > "$average_binding" || exit 1
 	check_non_empty "$average_binding" "average binding"
 
 	echo "  filtering mers that are not in the melting range ($min_melting_temp-$max_melting_temp)"
diff --git a/src/filter_average_binding.py b/src/filter_average_binding.py
index e526be8..97088b2 100755
--- a/src/filter_average_binding.py
+++ b/src/filter_average_binding.py
@@ -1,13 +1,21 @@
 #!/usr/bin/env python2.7
 import sys
+import argparse
 import os
 
 debug = os.environ.get("debug", False)
 
-from subprocess import Popen
-from subprocess import PIPE
-
 def get_length(fn):
+	'''
+		get the length of a fasta file by piping it through several unix 
+		programs.
+
+		1) remove headers by grepping for any ">" at the start of a line
+		2) delete all occurances of a new line, to join sequences together
+		3) sum the number of characters.
+	'''
+	from subprocess import Popen
+	from subprocess import PIPE
 
 	cmd = 'grep "^>" ' + fn + " -v | tr -d '\\n' | wc -c"
 
@@ -19,17 +27,36 @@ def get_length(fn):
 
 	return int(points_fh.stdout.readline())
 
-if len(sys.argv) < 2:
-	print "filter_average_binding.py foreground.fa binding_distance"
-	exit()
-	
-foreground = sys.argv[1]
-distance = int(sys.argv[2])
+def main(): 
+	'''
+	This filter removes mers where the count / (length of the genome) is below a
+	certain threshold as specified by -m
+	'''
+
+	parser = argparse.ArgumentParser(description="Filter mers where (k-mer count / length of the genome) < minimum") 
+	parser.add_argument("-f", "--fasta", help="foreground fasta file", required=True )
+	parser.add_argument("-c", "--counts", help="kmer counts of the foreground fasta file", required=True )
+	parser.add_argument("-m", "--minimum", help="the minium average foreground binding distance", required=True, type=float)
+
+	args = parser.parse_args()
+
+	if not os.path.exists(args.fasta):
+		exit("foreground fasta file " + args.fasta + " not found.")
+
+	if not os.path.exists(args.counts):
+		exit("count file " + args.counts + " not found.")
+			
+
+	# get genome length
+	genome_length = float(get_length(args.fasta))
+
+	count_fh = open(args.counts, "rU")
 
-genome_length = get_length(foreground)
+	for line in count_fh:
+		(_, count) = line.split()
+		if (genome_length / float(count)) < args.minimum:
+			sys.stdout.write(line)
 
-for line in sys.stdin:
-	(mer, count) = line.split()
-	if (genome_length / int(count)) < distance:
-		sys.stdout.write(line)
+if __name__ == "__main__":
+	sys.exit(main())
 
-- 
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