fixing lowercase characters in reference

fmfi-compbio · Aug 30, 2023 · 846ace3 · 846ace3
1 parent d0374b2
commit 846ace3
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/src/schemas/locus.py b/src/schemas/locus.py
@@ -48,7 +48,8 @@ def __init__(
     def prepare_sequence(self, reference_path: str):
         fa_seq: str = pysam.faidx(reference_path, self.coord)
         seq = ''.join(fa_seq.split('\n')[1:])
-        noting_seq = ''.join(fa_seq.split('\n')[1:])
+        seq = seq.upper()
+        noting_seq = seq
         if len(seq) <= 1:
             raise ValueError(f'Reference repeat sequence is empty for {self.name} - check coord {self.coord}')
         if not self.motif: