minor cleanup in variable naming

functions.py

@@ -102,9 +102,9 @@ def check_overlap(pfd_matrix, overlap_cutoff):
             if row1[-1] == row2[-1]:
                 #check if there is overlap between the domains
                 if no_overlap(int(row1[3]), int(row1[4]), int(row2[3]), int(row2[4])) == False:
-                    overlapping_nucleotides = overlap(int(row1[3]), int(row1[4]), int(row2[3]), int(row2[4]))
-                    overlap_perc_loc1 = overlap_perc(overlapping_nucleotides, int(row1[4])-int(row1[3]))
-                    overlap_perc_loc2 = overlap_perc(overlapping_nucleotides, int(row2[4])-int(row2[3]))
+                    overlapping_aminoacids = overlap(int(row1[3]), int(row1[4]), int(row2[3]), int(row2[4]))
+                    overlap_perc_loc1 = overlap_perc(overlapping_aminoacids, int(row1[4])-int(row1[3]))
+                    overlap_perc_loc2 = overlap_perc(overlapping_aminoacids, int(row2[4])-int(row2[3]))
                     #check if the amount of overlap is significant
                     if overlap_perc_loc1 > overlap_cutoff or overlap_perc_loc2 > overlap_cutoff:
                         if float(row1[1]) >= float(row2[1]): #see which has a better score
@@ -133,6 +133,8 @@ def check_overlap(pfd_matrix, overlap_cutoff):
         loci_end = int(row[8])
         domain_start = int(row[3])
         domain_end = int(row[4])
+        
+        # uses nucleotide coordinates for sorting
         width = 3*(domain_end - domain_start)
         strand = row[9].split(":")[-1]
         if strand == "+":
@@ -569,4 +571,4 @@ def get_composite_bgc_similarities(bgcs_1, bgcs_2, sim_matrix):
             if (sim > max_sim[0]):
                 max_sim = (sim, bgc_1, bgc_2) if (bgc_2 > bgc_1) else (sim, bgc_2, bgc_1)
             num_pairs += 1
-    return ((sum_sim / num_pairs), min_sim, max_sim) # let it throw infinite division error by itself
\ No newline at end of file
+    return ((sum_sim / num_pairs), min_sim, max_sim) # let it throw infinite division error by itself