split

2 files changed, 15 insertions, 23 deletions

diff --git a/score_mers.py b/score_mers.py
index 3409fc0..0a73cfb 100755
--- a/score_mers.py
+++ b/score_mers.py
@@ -10,11 +10,11 @@ import pdb
 fg_mers = {}
 bg_mers = {}
 
-if(len(sys.argv) == 4):
+if(len(sys.argv) == 5):
 	selectivity_fn =  sys.argv[1]
-	fg_fasta_fn =  sys.argv[2]
-	bg_fasta_fn =  sys.argv[3]
-	output_file =  sys.argv[4]
+	fg_fasta_fn    =  sys.argv[2]
+	bg_fasta_fn    =  sys.argv[3]
+	output_file    =  sys.argv[4]
 else:
 	print "please specify your inputs"
 	print "ex: select_mers.py fg_counts_file fg_fasta_file bg_counts_file bg_fasta_file output_file"
@@ -139,17 +139,19 @@ def pop_bg(mer):
 def main():
 	import time
 	selected = []
-	selectivty_fh = open(selectivity_fn, "r")
+	selectivity_fh = open(selectivity_fn, "r")
 	
 	# get our genome length
 	fg_genome_length = os.path.getsize(fg_fasta_fn)
 	bg_genome_length = os.path.getsize(bg_fasta_fn)
 
-	for row in selectivity_fn:
+	for row in selectivity_fh:
 		(mer, fg_count, bg_count, selectivity) = row.split()
 		fg_mers[mer] = Mer()
+		fg_mers[mer].pts = []
 		fg_mers[mer].count = fg_count
 		bg_mers[mer] = Mer()
+		bg_mers[mer].pts = []
 		bg_mers[mer].count = bg_count
 		selected.append([mer, selectivity])
 		
@@ -160,6 +162,7 @@ def main():
  	# else:
   #		selected = select_mers(fg_mers, bg_mers, max_select)
  	selected =	selected[-100:] 
+	selected_mers = [row[0] for row in selected]
 	pdb.set_trace()
 	#	print "searching through combinations of"
 	#	print selected
@@ -167,10 +170,10 @@ def main():
 	print "Populating foreground locations"
 
 
-	map(pop_fg, selected)
-	map(pop_bg, selected)
+	map(pop_fg, selected_mers)
+	map(pop_bg, selected_mers)
 
-	scores = score_mers(selected)
+	scores = score_mers(selected_mers)
 
 	print "fg_genome_length", fg_genome_length
 	print "bg_genome_length", bg_genome_length
diff --git a/select_mers.py b/select_mers.py
index a4657d4..21306cc 100755
--- a/select_mers.py
+++ b/select_mers.py
@@ -33,13 +33,13 @@ def select_mers(fg_mers, bg_mers):
 	# populate our bg_arr and fg_arr as well as our mer arr.
 	for mer in fg_mers.keys():
 		mers.append(mer);
-		bg_arr.append(bg_mers[mer] + 1);
+		bg_arr.append(bg_mers.get(mer, 1));
 		fg_arr.append(fg_mers[mer]);
 
 	fg_arr = np.array(fg_arr, dtype='f');
 	bg_arr = np.array(bg_arr, dtype='f');
 
-	selectivity = (fg_arr/fg_genome_length) / (bg_arr/bg_genome_length)
+	selectivity = (fg_arr / bg_arr)
 
 	arr = [(mers[i], fg_arr[i], bg_arr[i], selectivity[i]) for i in range(len(mers))]
 
@@ -55,40 +55,29 @@ def select_mers(fg_mers, bg_mers):
 
 def main():
 
-
 	fg_count_fh = open(fg_count_fn, "r")
 	bg_count_fh = open(bg_count_fn, "r")
 	
 	# copy in our fg_mers and counts
-	print "populating our mers dictionary"
 	for mers,fh in [(fg_mers, fg_count_fh), (bg_mers, bg_count_fh)]:
 		for line in fh:
 			(mer, count) = line.split()
 			mers[mer] = int(count)
 	
 	if min_mer_count >= 1:
-		print "removing that are less frequent than: ", min_mer_count
 		for mer in fg_mers.keys():
 			if(fg_mers[mer] < min_mer_count):
 				del fg_mers[mer]
 				if mer in bg_mers:
 					del bg_mers[mer]
 	
-	print "removing useless mers from the background"
 	for mer in bg_mers.keys():
 		if mer not in fg_mers:
 			del bg_mers[mer]
 
-	print "adding empty mers to the background"
-	for mer in fg_mers:
-		if mer not in bg_mers:
-			bg_mers[mer] = 0
-
-	print fg_genome_length
-	print bg_genome_length
 	selected = select_mers(fg_mers, bg_mers)
 	for row in selected:
-		print row[0] +"\t"+str(row[1]) + "\t" + str(row[2]) + str(row[3])
+		print row[0] +"\t"+str("%d" % row[1]) + "\t" + str("%d" % row[2]) + "\t" + str("%.5f" % row[3])
 
 if __name__ == "__main__":
 	sys.exit(main())