DB creation can now handle edge cases

db_building/TrainingRead.py

@@ -196,6 +196,15 @@ class TrainingRead(Persistent):
                     width_l -= random_offset
                     width_r += random_offset
                 mid_idx = ch[1] + len(ch[2])//2
+                # Handle edge cases
+                if width_l > mid_idx:
+                    # Cannot cut off enough on left side
+                    width_l = mid_idx
+                    width_r = width - width_l
+                elif width_r > len(self.raw) - mid_idx:
+                    # Cannot cut off enough on right side
+                    width_r = len(self.raw) - mid_idx
+                    width_l = width - width_r
                 candidate_raw = self.raw[mid_idx - width_l:
                                          mid_idx + width_r]
                 kmer_in_read = np.all(np.in1d(ch[2], candidate_raw))
@@ -221,14 +230,16 @@ class TrainingRead(Persistent):
             pos_kmer_seqs = [pos_event[2] for pos_event in pos_events]
             # Make sure the negative examples are far enough away from
             # the target k mer (manually add 30 to be extra safe).
+            idx_list.remove(cur_idx)
             if np.all(np.array(distances_to_kmer) > width):
                 mid_idx = cur_condensed_event[1] + len(cur_condensed_event[2])//2
                 candidate_raw = self.raw[mid_idx - width_l:mid_idx + width_r]
                 target_kmer_in_read = np.all([np.in1d(pos_raw, candidate_raw)
                                               for pos_raw in pos_kmer_seqs])
-                assert not target_kmer_in_read, 'Target kmer in negative read'
+                if target_kmer_in_read:
+                    # Something went wrong (probably edge case (that I should fix)), try again
+                    continue
                 raw_hits_out.append(candidate_raw)
                 raw_kmers_out.append(cur_condensed_event[0])
 
-            idx_list.remove(cur_idx)
         return raw_hits_out, raw_kmers_out

train_nn.py

 import random
 import re
+from collections import Counter
+
 import yaml
 import pickle
 import importlib