From 37b00ef174203dfb914aaca6feed8da54d4f1979 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Tue, 25 Mar 2014 13:30:49 -0400 Subject: remove stray ; --- src/score_mers.py | 45 +++++++++++++++++++++++---------------------- 1 file changed, 23 insertions(+), 22 deletions(-) diff --git a/src/score_mers.py b/src/score_mers.py index c2e18ff..ac7564d 100755 --- a/src/score_mers.py +++ b/src/score_mers.py @@ -31,15 +31,15 @@ else: exit() # import our variables -cpus = int(os.environ.get("cpus", cpu_count())); -debug = int(os.environ.get("debug", False)); -min_mer_range = int(os.environ.get("min_mer_range", 6)); -max_mer_range = int(os.environ.get("max_mer_range", 12)); -min_mer_count = int(os.environ.get("min_mer_count", 0)); -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)); -max_consecutive_binding = int(os.environ.get("max_consecutive_binding", 4)); +cpus = int(os.environ.get("cpus", cpu_count())) +debug = int(os.environ.get("debug", False)) +min_mer_range = int(os.environ.get("min_mer_range", 6)) +max_mer_range = int(os.environ.get("max_mer_range", 12)) +min_mer_count = int(os.environ.get("min_mer_count", 0)) +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)) +max_consecutive_binding = int(os.environ.get("max_consecutive_binding", 4)) def get_max_consecutive_binding(mer1, mer2): @@ -66,7 +66,7 @@ def get_max_consecutive_binding(mer1, mer2): # pad mer one to avoid errors mer1 = mer1.ljust(mer1_len + len(mer2), "_") - max_bind = 0; + max_bind = 0 for offset in range(mer1_len): consecutive = 0 for x in range(len(mer2)): @@ -134,7 +134,7 @@ def filter_mers(combination): return False def check_feasible(selected): - total = 0; + total = 0 for mer in selected: total += len(fg_mers[mer]) if (fg_genome_length / (total + 1 )) > max_mer_distance: @@ -147,32 +147,33 @@ def check_feasible(selected): def score_mers(selected): import time - total_scored = 0; + total_scored = 0 check_feasible(selected) p = Pool(cpus) - fh = open(output_file, 'wb'); - fh.write("Combination\tScore\tFG_mean_dist\tFG_stdev_dist\tBG_mean_dist\tBG_var_dist\n"); + fh = open(output_file, 'wb') + fh.write("Combination\tScore\tFG_mean_dist\tFG_stdev_dist\tBG_mean_dist\tBG_var_dist\n") + for select_n in range(1, max_select+1): print "scoring size ", select_n, t = time.time() scores_it = p.imap_unordered(score, combinations(selected, select_n), chunksize=8192) for score_res in scores_it: if score_res is not None: - total_scored += 1; - combination, scores, fg_mean_dist, fg_stddev_dist, bg_ratio = score_res - fh.write(str(combination) + "\t"); - fh.write(str(scores) + "\t"); - fh.write(str(fg_mean_dist) + "\t"); - fh.write(str(fg_stddev_dist) + "\t"); - fh.write(str(bg_ratio) + "\n"); + total_scored += 1 + combination, score_val, fg_mean_dist, fg_stddev_dist, bg_ratio = score_res + fh.write(str(combination) + "\t") + fh.write(str(score_val) + "\t") + fh.write(str(fg_mean_dist) + "\t") + fh.write(str(fg_stddev_dist) + "\t") + fh.write(str(bg_ratio) + "\n") print "size ", select_n, "took:", time.time() - t if(total_scored == 0): print "NO RESULTS FOUND" - fh.write("NO RESULTS FOUND\n"); + fh.write("NO RESULTS FOUND\n") heterodimer_dic = {} def score(combination): -- cgit v1.2.3