bg ratio

4 files changed, 13 insertions, 3 deletions

diff --git a/README.md b/README.md
index 0dbe2b5..b18b21a 100644
--- a/README.md
+++ b/README.md
@@ -164,6 +164,7 @@ max\_mer\_distance | 5000 | maximum distance between mers in foreground
 min\_melting\_temp | 0° | minimum melting temp of mers
 max\_melting\_temp | 30° | maximum melting temp of mers
 min\_foreground\_binding\_average | 50000 | eliminate mers that appear less frequently than the average  (length of foreground / # of occurrances)
+min\_bg\_ratio | Not Enabled | eliminate mers where the background ration is less than the minimum
 ignore\_mers | Not Enabled | mers to explicitly ignore, space separated ex. ignore\_mers="ACAGTA ACCATAA ATATATAT"
 ignore\_all\_mers\_from\_files | Not Enabled | ignore any mers found in these files. space separated.
 output\_directory | $foreground\_$background/ | ex. if fg is Bacillus.fasta and  bg is HumanGenome.fasta then folder would be $PWD/Bacillus.fasta\_HumanGenome\_output.fasta/
diff --git a/SelectiveWholeGenomeAmplification b/SelectiveWholeGenomeAmplification
index 23b14bc..7a3d46b 100755
--- a/SelectiveWholeGenomeAmplification
+++ b/SelectiveWholeGenomeAmplification
@@ -179,6 +179,9 @@ done
 # sort score by the minimum or maximum value. acceptable parameters are min or max.
 : ${sort_by="min"}
 
+# bg_ratio
+: ${min_bg_ratio=0}
+
 export ignore_mers
 export min_mer_range
 export max_mer_range
@@ -194,8 +197,6 @@ export min_melting_temp
 export fg_weight
 export primer_weight
 
-
-echo
 # check foreground and background
 if [[ ! -f "$foreground" ]]; then
 	echo "Error: could not open foreground: $foreground"
diff --git a/SelectiveWholeGenomeAmplificationUI b/SelectiveWholeGenomeAmplificationUI
index b6514a9..5eb0049 100755
--- a/SelectiveWholeGenomeAmplificationUI
+++ b/SelectiveWholeGenomeAmplificationUI
@@ -53,6 +53,10 @@ questions = [
 	  'def': "5000 bases",
 	  'v': 'max_mer_distance' },
 
+	{ 'q': 'minimum background ratio?',
+	  'def': "None",
+	  'v': 'min_bg_ratio' },
+
 	{ 'q': 'maximum melting temperature for mers?', 'def': '30c', 'v': 'max_melting_temp' },
 	{ 'q': 'minimum melting temperature for mers?', 'def': '0c',  'v': 'min_melting_temp' },
 	{ 'q': 'DNA Concentration (nM)?', 'def': '5000nM',  'v': 'dna_con' },
diff --git a/src/score_mers.py b/src/score_mers.py
index 7d265a3..65e7dc1 100755
--- a/src/score_mers.py
+++ b/src/score_mers.py
@@ -32,6 +32,7 @@ debug            = os.environ.get("debug", False)
 max_select       = int(os.environ.get("max_select", 15))
 max_check        = int(os.environ.get("max_check", 35))
 max_mer_distance = int(os.environ.get("max_mer_distance", 5000))
+min_bg_ratio     = int(os.environ.get("min_bg_ratio", 0))
 max_consecutive_binding = int(os.environ.get("max_consecutive_binding", 4))
 primer_weight = float(os.environ.get("primer_weight", 0))
 score_str = os.environ.get("score_func", None)
@@ -233,6 +234,7 @@ def print_rejected(total_reject, total_checked, total_scored, excluded):
 	print "  max distance: " + percentage(excluded[0], total_reject) + " (" + str(excluded[0]) + ")"
 	print "  mers overlap: " + percentage(excluded[1], total_reject) + " (" + str(excluded[1]) + ")"
 	print "  heterodimers: " + percentage(excluded[2], total_reject) + " (" + str(excluded[2]) + ")"
+	print "  min bg ratio: " + percentage(excluded[3], total_reject) + " (" + str(excluded[3]) + ")"
 	print ""
 	print "  total combinations checked: ", total_checked
 	print "  total combinations scored:  ", total_scored
@@ -243,7 +245,7 @@ def score_specific_combinations(mers):
 
 	total_scored = 0
 	total_checked = 0
-	excluded = [0, 0, 0]
+	excluded = [0, 0, 0, 0]
 
 	p = Pool(cpus)
 
@@ -352,6 +354,8 @@ def score(combination):
 
 	bg_ratio = (bg_genome_length / bg_counts)
 
+	if(bg_ratio < min_bg_ratio)
+		return 3
 
 	nb_primers = len(combination)
 	fg_mean_dist = np.mean(fg_dist)