New bin logic now properly works :)

lib/scripts/generate_pairs.py

@@ -61,8 +61,9 @@ MESSAGE("Bin specification is " + param(binspec))
 STEP("Parsing bin specification")
 try:
     binspec = binspec.split("],[")
+    nb_bins = len(binspec)
     binspec[0] = binspec[0][1:] # removing [ and ] at the beginning and end
-    binspec[len(binspec)-1] = binspec[len(binspec)-1][:-1]
+    binspec[nb_bins-1] = binspec[nb_bins-1][:-1]
     binspec = list(map(lambda i: list(map(float, i.split(","))), binspec))
 
     if False in list(map(lambda i: len(i) == 2, binspec)):
@@ -75,12 +76,12 @@ try:
     else:
         SUCCESS("All intervals seem to be properly constructed.")
 
-    for i in range(len(binspec) - 1):
+    for i in range(nb_bins - 1):
         if binspec[i][1] > binspec[i+1][0]:
             FAILURE("Bins do not seem to be disjoint and/or are not in ascending order.")
     SUCCESS("Bins are disjoint and in ascending order.")
 
-    MESSAGE("Found " + data(len(binspec)) + " bins")
+    MESSAGE("Found " + data(nb_bins) + " bins")
     list(map(lambda i: SUBMESSAGE("from " + data(i[0]) + " to " + data(i[1])), binspec))
 except:
     FAILURE("Bin specification was improperly formatted!")
@@ -116,6 +117,9 @@ from math import sqrt
 def pick(profiles): # returns a profile in the form of a numpy array
     return profiles.sample().values[0]
 
+def in_bin(dist, i):
+    return binspec[i][0] <= dist and binspec[i][1] >= dist;
+
 def euclidian_distance(p1, p2):
     return norm(p1 - p2)
 
@@ -128,48 +132,40 @@ def jensen_shannon_divergence(p1, p2): # https://stackoverflow.com/questions/158
 def jensen_shannon_distance(p1, p2):
     return sqrt(jensen_shannon_divergence(p1, p2))
 
-MESSAGE("Preparing dataframe...")
+MESSAGE("Preparing a dataframe for every bin...")
 columns = ["p1_" + str(i) for i in range(20)] + ["p2_" + str(i) for i in range(20)] + ["distance"]
-pairs = pd.DataFrame(columns = columns)
+pair_bins = [pd.DataFrame(columns = columns) for x in range(nb_bins)]
 
 MESSAGE("Picking profile pairs and computing distances...")
-nb_pairs = 300
-try:
-    import progressbar
-    bar = progressbar.ProgressBar()
-    myrange = bar(range(nb_pairs))
-except:
-    myrange = range(nb_pairs)
-    print("-- Progressbar is not installed! Cannot display progress. Please wait for a while...")
-
-for i in myrange:
+nb_pairs_per_bin = 100
+while min(map(lambda b: b.shape[0], pair_bins)) < nb_pairs_per_bin:
     p1 = pick(profiles)
     p2 = pick(profiles)
-    # dist = jensen_shannon_divergence(p1, p2)
     dist = jensen_shannon_distance(p1, p2)
+    # dist = jensen_shannon_divergence(p1, p2)
     # dist = euclidian_distance(p1, p2)
-    new_row = p1.tolist() + p2.tolist() + [dist]
-    pairs.loc[len(pairs)] = new_row
 
-# pairs["distance"].hist(bins = 40)
-# plt.show()
+    for i in range(nb_bins):
+        if in_bin(dist, i) and pair_bins[i].shape[0] < nb_pairs_per_bin:
+            new_row = p1.tolist() + p2.tolist() + [dist]
+            pair_bins[i].loc[len(pair_bins[i])] = new_row
+            break
+
+MESSAGE("Post-treatment of pair bins...")
+for i in range(nb_bins):
+    pair_bins[i].sort_values(by=["distance"])
+    pair_bins[i]["distance"].hist(bins = 40)
+plt.show()
 
 #===================================================================================================
 print(step("Writing result to file"))
 from numpy import array_split
 
-MESSAGE("Sorting pairs by distance...")
-pairs = pairs.sort_values(by=["distance"])
-
-MESSAGE("Separating pairs into chunks...")
-nb_classes = 3
-chunks = array_split(range(nb_pairs), nb_classes)
-
-for i in range(nb_classes):
+for i in range(nb_bins):
     filename_out = out + "_" + str(i) + ".tsv"
     MESSAGE("Writing pairs to " + param(filename_out))
-    columns[0] = "#p1_0"
+    # columns[0] = "#p1_0"
     #pairs.iloc[chunks[i]].to_csv(filename_out, sep='\t', index=False, header=columns)
-    pairs.iloc[chunks[i]].to_csv(filename_out, sep='\t', index=False, header=False)
+    pair_bins[i].to_csv(filename_out, sep='\t', index=False, header=False)
 
 MESSAGE("Done :)")