Fix #181 and small bug fix for parsing Mikado annotations.

EI-CoreBioinformatics · Jun 10, 2019 · 94160dd · 94160dd
1 parent 468eb2c
commit 94160dd
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diff --git a/Mikado/parsers/bed12.py b/Mikado/parsers/bed12.py
@@ -500,7 +500,8 @@ def _adjust_start(self, sequence, orf_sequence):
                     self.phase = 0
             else:
                 if self.end - self.thick_end <= 2:
-                    self.phase = self.end - self.thick_end
+                    new_phase = max(self.end - self.thick_end, 0)
+                    self.phase = new_phase
                     self.thick_end = self.end
                 else:
                     self.phase = 0

diff --git a/Mikado/parsers/gfannotation.py b/Mikado/parsers/gfannotation.py
@@ -240,6 +240,8 @@ def is_gene(self):
             elif self.id is not None and self.id.startswith("gene:"):
                 # Hack for EnsEMBL
                 return True
+            elif self.feature in ("sublocus", "monosublocus", "monosublocusholder"):
+                return True
         return False
 
     @property