diff options
Diffstat (limited to 'src/score_mers.py')
| -rwxr-xr-x | src/score_mers.py | 6 |
1 files changed, 5 insertions, 1 deletions
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) |