From c310094c5fbe9ea5c98315b61622c38fa8c3cf5a Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 29 May 2024 15:26:05 +0000
Subject: [PATCH] formatting, bugfix, remove prints

---
 anglerfish/anglerfish.py    |  3 ++-
 anglerfish/demux/adaptor.py | 13 ++++---------
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/anglerfish/anglerfish.py b/anglerfish/anglerfish.py
index b346f6e..0ce1337 100755
--- a/anglerfish/anglerfish.py
+++ b/anglerfish/anglerfish.py
@@ -277,7 +277,8 @@ def run_demux(args):
             sample_dists = [
                 (
                     lev.distance(
-                        i[0], f"{x.adaptor.i7.index_seq}+{x.adaptor.i5.index_seq}".lower()
+                        i[0],
+                        f"{x.adaptor.i7.index_seq}+{x.adaptor.i5.index_seq}".lower(),
                     ),
                     x.sample_name,
                 )
diff --git a/anglerfish/demux/adaptor.py b/anglerfish/demux/adaptor.py
index 6e0cf87..74184b6 100644
--- a/anglerfish/demux/adaptor.py
+++ b/anglerfish/demux/adaptor.py
@@ -64,7 +64,6 @@ class AdaptorPart:
 
     def __init__(self, sequence_token: str, name: str, index_seq: str | None):
         # Assign attributes from args
-        print(name, sequence_token, index_seq)
         self.sequence_token: str = sequence_token
         self.name: str = name
         self.index_seq: str | None = index_seq
@@ -133,14 +132,13 @@ def __init__(self, sequence_token: str, name: str, index_seq: str | None):
             self.len_umi_before_index = 0
             self.len_umi_after_index = 0
             self.len_before_index = len(split_by_index[0])
-            self.len_after_index = len(split_by_index[1])
+            self.len_after_index = len(split_by_index[-1])
 
         elif not self.has_index and self.has_umi:
             # No index, UMI
-            self.len_umi_before_index = None
-            self.len_umi_after_index = None
-            self.len_before_index = len(split_by_index[0])
-            self.len_after_index = len(split_by_index[1])
+            raise UserWarning(
+                f"Adaptor {self.name} has UMI but no index. This is not supported."
+            )
 
         else:
             # No index, no UMI
@@ -149,9 +147,6 @@ def __init__(self, sequence_token: str, name: str, index_seq: str | None):
             self.len_before_index = None
             self.len_after_index = None
 
-        # Sanity check
-        print(self.__dict__)
-
     def get_mask(self, insert_Ns: bool = True) -> str:
         """Get the mask of the adaptor part.