really reduce memory usage of select_mers.py

2 files changed, 38 insertions, 40 deletions

diff --git a/src/score_mers.py b/src/score_mers.py
index 9d90ae2..0ddeb91 100755
--- a/src/score_mers.py
+++ b/src/score_mers.py
@@ -487,6 +487,8 @@ def main():
 
 		# load it into our fg and bg counts into their dictionaries
 		for mer in selected_mers:
+			if mer.startswith("#"):
+				continue
 			split_mer = mer.split()
 			fg_mers[split_mer[0]] = []
 			bg_mers[split_mer[0]] = int(split_mer[2])
@@ -494,7 +496,7 @@ def main():
 		selected_mers = [x.split()[0] for x in selected_mers]
 
 		if len(selected_mers) is 0:
-			print "no merss found."
+			print "no mers found."
 			exit(1)
 
 		# we already have our background counts
@@ -511,6 +513,8 @@ def main():
 
 		combination_fh = open(args.combination_file, "r")
 		for line in combination_fh:
+			if line.startswith("#"):
+				continue
 			mers = line.split()
 			combinations.append(mers)
 			for mer in mers:
@@ -529,6 +533,8 @@ def main():
 
 		mer_fh = open(args.mer_file, "r")
 		for mer in mer_fh:
+			if mer.startswith("#"):
+				continue
 			mer = mer.strip()
 			if(len(mer.split()) > 1):
 				print "skipping line:", mer, "each line should contain only one mer"
diff --git a/src/select_mers.py b/src/select_mers.py
index 5f42717..ceec4a0 100755
--- a/src/select_mers.py
+++ b/src/select_mers.py
@@ -2,58 +2,50 @@
 import sys
 import os
 
-fg_mers = {}
-bg_mers = {}
-
 fg_weight = float(os.environ.get("fg_weight", 0))
 max_check = int(os.environ.get("max_check", 0))
 
-if(len(sys.argv) == 3):
-	fg_count_fn =  sys.argv[1]
-	bg_count_fn =  sys.argv[2]
-else:
-	print len(sys.argv)
-	sys.stderr.write("please specify your inputs\n")
-	sys.stderr.write("ex: select_mers.py fg_counts bg_count\n")
-	exit(1)
-
-
-# select mers based on our 'selectivity' measure. (count in fg) / (count in bg)
-def select_mers(fg_mers, bg_mers):
-
-	# populate our bg_arr and fg_arr as well as our mer arr.
-
-	score = {}
-
-	for mer in fg_mers.keys():
-		score[mer] = (fg_mers[mer] / bg_mers[mer]) * (fg_mers[mer]**fg_weight)
 
-	sorted_scored_mers =	sorted(score, key=score.get)
-
-	for mer in sorted_scored_mers: 
-		print mer, int(fg_mers[mer]), int(bg_mers[mer]), (fg_mers[mer] / bg_mers[mer]) * (fg_mers[mer]**fg_weight)
+def main():
 
+	if(len(sys.argv) == 3):
+		fg_count_fn =  sys.argv[1]
+		bg_count_fn =  sys.argv[2]
+	else:
+		sys.stderr.write("please specify your inputs\n")
+		sys.stderr.write("ex: select_mers.py fg_counts bg_count\n")
+		exit(1)
 
-def main():
+	# mers dictionary:
+	# 
+	# Key: mer name, eg AAAACT 
+	# Value: fg_mer_count, bg_mer_count
+	mers = {}
 
 	fg_count_fh = open(fg_count_fn, "r")
 	bg_count_fh = open(bg_count_fn, "r")
 	
-	# copy in our fg_mers and counts
-	for mers,fh in [(fg_mers, fg_count_fh), (bg_mers, bg_count_fh)]:
-		for line in fh:
-			(mer, count) = line.split()
-			mers[mer] = float(count)
+	# copy in our foreground mers and counts into mers dictionary
+	for line in fg_count_fh:
+		(mer, count) = line.split()
+		mers[mer] = [float(count), 1]
 	
-	for mer in fg_mers.keys():
-		if mer not in bg_mers:
-			bg_mers[mer] = 1
+	
+	for line in bg_count_fh:
+		(mer, count) = line.split()
+		if mer in mers:
+			mers[mer][1] = float(count)
+
+	score = []
+
+	for mer in mers:
+		score.append([mer, (mers[mer][0] / mers[mer][1]) * (mers[mer][0]**fg_weight)])
 
-	for mer in bg_mers.keys():
-		if mer not in fg_mers:
-			del bg_mers[mer]
+	sorted_scored_mers = sorted(score, key=lambda x: x[1])
 
-	selected = select_mers(fg_mers, bg_mers)
+	sys.stdout.write('#MERS\tFG_COUNT\tBG_COUNT\tSCORE\n')
+	for scores in sorted_scored_mers: 
+		sys.stdout.write(scores[0] + '\t' + str(int(mers[scores[0]][0])) + '\t' +  str(int(mers[scores[0]][1])) + '\t' +  str(scores[1])+ '\n')
 
 if __name__ == "__main__":
 	sys.exit(main())