diff options
Diffstat (limited to 'src/score_mers.py')
| -rwxr-xr-x | src/score_mers.py | 28 |
1 files changed, 10 insertions, 18 deletions
diff --git a/src/score_mers.py b/src/score_mers.py index ba63f71..1d3456b 100755 --- a/src/score_mers.py +++ b/src/score_mers.py @@ -204,35 +204,27 @@ def score(combination): #return [combination, "max", max(fg_dist)] return None - min_mer_distance = max(len(i) for i in combination) - # return without calculating scores if any mers are closer than the length of - # our longest mer in the combination - if any(dist < min_mer_distance for dist in fg_dist): - #return [combintaion, 'max'] - return None - - - # bg points - bg_pts = [] - bg_dist = [] + # bg counts + bg_counts = 0 for mer in combination: - bg_pts = bg_pts + bg_mers[mer] + bg_counts += len(bg_mers[mer]) - if len(bg_pts()) <= 1: - bg_pts.append(0, 1, fg_genome_length) + if bg_counts <= 1: + bg_counts = 1 - bg_sum = sum(bg_pts) - bg_ratio = (bg_genome_length / bg_sum) + bg_sum = len(bg_counts) + bg_ratio = (bg_genome_length / bg_sum) nb_primers = len(combination) fg_mean_dist = np.mean(fg_dist) fg_std_dist = np.std(fg_dist) + # this is our equation - score = (nb_primers * fg_mean_dist * fg_std_dist) / bg_ratio + mer_score = (nb_primers * fg_mean_dist * fg_std_dist) / bg_ratio - return [combination, score, fg_mean_dist, fg_std_dist, bg_ratio] + return [combination, mer_score, fg_mean_dist, fg_std_dist, bg_ratio] def load_end_points(fn): |