Minor BugFix for DIAMOND XML parsing < 0.9.31

EI-CoreBioinformatics · Apr 7, 2020 · e6f3be6 · e6f3be6
1 parent b3f3d7a
commit e6f3be6
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/Mikado/serializers/blast_serializer/hit.py b/Mikado/serializers/blast_serializer/hit.py
@@ -330,12 +330,12 @@ def prepare_hit(hit, query_id, target_id, off_by_one=False, as_list=False, **kwa
                 list(ident[(ident < 0)]),
                 list(ident[ident > query_array.shape[1]])))
         try:
-            query_array[0, ident] = 1
+            query_array[0, ident - off_by_one] = 1
         except IndexError as exc:
             raise IndexError("{}, off by one: {}; min, max: {}, {}; hsp {}".format(
                 exc, off_by_one, ident.min(), ident.max(), hsp._items[0].__dict__))
         try:
-            query_array[1, posit] = 1
+            query_array[1, posit - off_by_one] = 1
         except IndexError as exc:
             raise IndexError("{}, off by one: {}; min, max: {}, {}; frame: {}".format(
                 exc, off_by_one, posit.min(), posit.max(), hsp.query_frame))

diff --git a/Mikado/serializers/blast_serializer/xml_utils.py b/Mikado/serializers/blast_serializer/xml_utils.py
@@ -20,7 +20,7 @@ def get_off_by_one(record):
             macro, minor, micro = [int(_) for _ in version.split(".")]
         except (ValueError, TypeError):
             return False
-        if macro > 0 or minor > 9 or micro > 30:
+        if macro > 0 or minor > 9 or (micro > 30 or micro < 25):
             return False
         else:
             return True