Performance

performance_test.py

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+import RF
+from ete3 import Tree
+import time
+import os
+import csv
+import logging
+
+logging.basicConfig(format='%(asctime)s - %(message)s', level=logging.INFO)
+
+
+def time_tree(newick):
+    tree = Tree(newick)
+    t0 = time.time()
+    sum3_dt = RF.polynomial_sum3_performance(tree, tree.get_leaves().__len__() + 1)[1]
+    tf = time.time()
+    return tf - t0, sum3_dt
+
+
+performance_test_directory = 'TreePerformanceTest/'
+treeset_performances = {}
+files = sorted(os.listdir(performance_test_directory))
+logging.info("Filenames loaded.")
+logging.info("Begin performance testing.")
+time.sleep(0.1)
+for i, filename in enumerate(files):
+    print("Scanning " + str(i) + " out of " + str(files.__len__()) + " files. [" + str(
+        ((i + 1) / files.__len__()) * 100)[0:5] + "%]")
+    if filename.endswith(".tre"):
+        print("Running performance test on " + filename)
+        f = open(performance_test_directory + filename)
+        lines = f.read()
+        tree_name = filename[0:filename.find("_")]
+        if tree_name not in treeset_performances:
+            treeset_performances[tree_name] = [""], ["T_poly"], ["T_con"]
+        treeset_performances[tree_name][0].append("tree" + filename[filename.find("_") + 1:filename.find(".")])
+        dt, sum3_dt = time_tree(lines)
+        treeset_performances[tree_name][1].append(dt)
+        treeset_performances[tree_name][2].append(sum3_dt)
+    else:
+        logging.info("Skipping " + filename + " because is not a .tre file.")
+logging.info("Finish performance test. Writing to file...")
+for key in treeset_performances.keys():
+    labels = treeset_performances[key][0]
+    T_poly_times = treeset_performances[key][1]
+    T_con_times = treeset_performances[key][2]
+    new_filename = 'performance_results/M' + key[4:] + '.csv'
+    logging.info("Writing to " + new_filename)
+    with open(new_filename, mode='w') as performance_file:
+        writer = csv.writer(performance_file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
+        writer.writerow(labels)
+        writer.writerow(T_poly_times)
+        writer.writerow(T_con_times)
+logging.info("Finish writing results to files. Find results in " + os.getcwd() + "/performance_results")