From 48e071c3c4bdb8d9d9227ef05030b9af4395f437 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Mon, 31 Mar 2014 16:10:32 -0400 Subject: add scorign to header and paramters and such --- src/score_mers.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'src/score_mers.py') diff --git a/src/score_mers.py b/src/score_mers.py index 0633c3e..1cb4bbb 100755 --- a/src/score_mers.py +++ b/src/score_mers.py @@ -35,12 +35,13 @@ max_check = int(os.environ.get("max_check", 35)) max_mer_distance = int(os.environ.get("max_mer_distance", 5000)) max_consecutive_binding = int(os.environ.get("max_consecutive_binding", 4)) primer_weight = float(os.environ.get("primer_weight", 0)) -score_func = os.environ.get("score_fun", None) +score_str = os.environ.get("score_func", None) -if score_func is not None: - score_func = compile('mer_score = ' + score_func, '', 'exec') +if score_str is not None: + score_func = compile('mer_score = ' + score_str, '', 'exec') else: score_func = compile('mer_score = (nb_primers**primer_weight) * (fg_mean_dist * fg_std_dist) / bg_ratio', '', 'exec') + score_str = '(nb_primers**primer_weight) * (fg_mean_dist * fg_std_dist) / bg_ratio' def get_max_consecutive_binding(mer1, mer2): ''' @@ -197,6 +198,7 @@ def percentage(part, whole, precision=2): def write_header(fh): fh.write("# variables used: max_select=" + str(max_select) + " max_check=" + str(max_check) + " max_mer_distance=" + str(max_mer_distance) + " max_consecutive_binding=" + str(max_consecutive_binding) + " primer_weight=" + str(primer_weight) + "\n") + fh.write("# scoring function:" + str(score_str) + "\n") fh.write("nb_primers\tCombination\tScore\tFG_mean_dist\tFG_stdev_dist\tBG_ratio\n") def write_result(fh, score_res): combination, score_val, fg_mean_dist, fg_stddev_dist, bg_ratio = score_res -- cgit v1.2.3