Merge branch 'development'

EI-CoreBioinformatics · Oct 7, 2015 · 9aeda78 · 9aeda78
2 parents caf2165 + 8636ff8
commit 9aeda78
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Showing 2 changed files with 7 additions and 8 deletions.
diff --git a/mikado_lib/loci_objects/transcript.py b/mikado_lib/loci_objects/transcript.py
@@ -1271,9 +1271,7 @@ def __recalculate_hit(self, hit, boundary):
                 pass
             else:
                 hsp_dict_list.append(hsp)
-                if (hsp["hsp_evalue"] < best_hsp[0] or
-                        (hsp["hsp_evalue"] == best_hsp[0] and
-                                 hsp["hsp_bits"] > best_hsp[1])):
+                if (hsp["hsp_evalue"] < best_hsp[0]):
                     best_hsp = (hsp["hsp_evalue"], hsp["hsp_bits"])
 
                 q_intervals.append((hsp["query_hsp_start"], hsp["query_hsp_end"]))

diff --git a/mikado_lib/serializers/blast_serializer.py b/mikado_lib/serializers/blast_serializer.py
@@ -1060,9 +1060,7 @@ def prepare_hit(cls, hit, query_id, target_id, **kwargs):
             hsp_dict["hsp_length"] = hsp.align_length
             hsp_dict["hsp_bits"] = hsp.bits
             hsp_dict["hsp_evalue"] = hsp.expect
-            if (hsp_dict["hsp_evalue"] < best_hsp[0] or
-                    (hsp_dict["hsp_evalue"] == best_hsp[0] and
-                             hsp_dict["hsp_bits"] > best_hsp[1])):
+            if (hsp_dict["hsp_evalue"] < best_hsp[0]):
                 best_hsp = (hsp_dict["hsp_evalue"], hsp_dict["hsp_bits"])
 
             hsp_dict["query_id"] = query_id
@@ -1086,7 +1084,10 @@ def prepare_hit(cls, hit, query_id, target_id, **kwargs):
         hit_dict["target_end"] = t_merged_intervals[-1][1]
         hit_dict["global_identity"] = len(identical_positions) * 100 / q_aligned
         hit_dict["global_positives"] = len(positives) * 100 / q_aligned
-        assert hit_dict["evalue"] == best_hsp[0]
-        assert hit_dict["bits"] == best_hsp[1]
+        if hit_dict["evalue"] != best_hsp[0] or hit_dict["bits"] != best_hsp[1]:
+            raise ValueError("Discrepant evalue/bits for hsps and hit; best: {0}, reported {1}".format(
+                best_hsp,
+                (hit_dict["evalue"], hit_dict["bits"])
+            ))
 
         return hit_dict, hsp_dict_list