fix strand detection

ablab · Aug 31, 2023 · 4508be2 · 4508be2
1 parent 064ec5b
commit 4508be2
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/common.py b/src/common.py
@@ -713,8 +713,8 @@ def count_noncanonincal(introns, reference_region, strand, ref_region_start=0):
 def get_intron_strand(intron, reference_region, ref_region_start=1):
     intron_left_pos = intron[0] - ref_region_start
     intron_right_pos = intron[1] - ref_region_start
-    left_site = str(reference_region[intron_left_pos:intron_left_pos + 2])
-    right_site = str(reference_region[intron_right_pos - 1:intron_right_pos + 1])
+    left_site = str(reference_region[intron_left_pos:intron_left_pos + 2]).upper()
+    right_site = str(reference_region[intron_right_pos - 1:intron_right_pos + 1]).upper()
     is_fwd = (left_site, right_site) in CANONICAL_FWD_SITES
     is_rev = (left_site, right_site) in CANONICAL_REV_SITES