add filtering based on consecutive mer lengths

1 files changed, 0 insertions, 83 deletions

diff --git a/select_mers.py b/select_mers.py
deleted file mode 100755
index 21306cc..0000000
--- a/select_mers.py
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env python
-import sys
-import os
-
-fg_mers = {}
-bg_mers = {}
-
-min_mer_count = int(os.environ.get("min_mer_count", 0));
-
-if(len(sys.argv) == 5):
-	fg_count_fn =  sys.argv[1]
-	fg_fasta_fn =  sys.argv[2]
-	bg_count_fn =  sys.argv[3]
-	bg_fasta_fn =  sys.argv[4]
-
-	fg_genome_length = os.path.getsize(fg_fasta_fn)
-	bg_genome_length = os.path.getsize(bg_fasta_fn)
-else:
-	print len(sys.argv)
-	print "please specify your inputs"
-	print "ex: select_mers.py fg_counts fg_fasta bg_counts bg_fasta"
-	exit()
-
-
-# select mers based on our 'selectivity' measure. (count in fg) / (count in bg)
-def select_mers(fg_mers, bg_mers):
-	import numpy as np
-
-	mers   = [] # contains mer strings
-	fg_arr = [] # contains fg counts
-	bg_arr = [] # contains bg counts
-	
-	# 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.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 / bg_arr)
-
-	arr = [(mers[i], fg_arr[i], bg_arr[i], selectivity[i]) for i in range(len(mers))]
-
-	# filter results less than 1 ( indicates that the bg is more present than the fg)
-	# arr = filter(lambda i: i[3] > 1, arr)
-
-	# sort by the selectivity 
-	arr = sorted(arr, key = lambda row: row[3])
-
-	# return only our mers, without our selectivity scores
-	return arr
-
-
-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
-	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:
-		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]
-	
-	for mer in bg_mers.keys():
-		if mer not in fg_mers:
-			del bg_mers[mer]
-
-	selected = select_mers(fg_mers, bg_mers)
-	for row in selected:
-		print row[0] +"\t"+str("%d" % row[1]) + "\t" + str("%d" % row[2]) + "\t" + str("%.5f" % row[3])
-
-if __name__ == "__main__":
-	sys.exit(main())