introduce new attributes for total length and constant length and fix bug

Author: kedhammar

anglerfish/demux/adaptor.py

@@ -68,13 +68,7 @@ def __init__(self, sequence_token: str, name: str, index_seq: str | None):
         self.name: str = name
         self.index_seq: str | None = index_seq
 
-        # Type declaration of attributes to be assigned
-        self.len_before_index: int | None
-        self.len_after_index: int | None
-        self.len_umi_before_index: int | None
-        self.len_umi_after_index: int | None
-
-        # Index
+        # Index bool and len
         if has_match(INDEX_TOKEN, self.sequence_token):
             split_by_index = re.split(INDEX_TOKEN, self.sequence_token)
 
@@ -85,7 +79,7 @@ def __init__(self, sequence_token: str, name: str, index_seq: str | None):
             self.has_index = False
             self.len_index = 0
 
-        # UMI
+        # UMI bool and len
         umi_tokens = re.findall(UMI_TOKEN, self.sequence_token)
         if len(umi_tokens) > 1:
             raise UserWarning(
@@ -100,6 +94,14 @@ def __init__(self, sequence_token: str, name: str, index_seq: str | None):
             self.has_umi = False
             self.len_umi = 0
 
+        # Type declaration of attributes to be assigned
+        self.len_before_index: int | None
+        self.len_after_index: int | None
+        self.len_umi_before_index: int | None
+        self.len_umi_after_index: int | None
+        self.len_total: int | None
+        self.len_constant: int
+
         # Lengths
         if self.has_index and self.has_umi:
             # Index and UMI
@@ -147,6 +149,9 @@ def __init__(self, sequence_token: str, name: str, index_seq: str | None):
             self.len_before_index = None
             self.len_after_index = None
 
+        self.len_total = len(self.get_mask(insert_Ns=True)) if self.index_seq else None
+        self.len_constant = len(self.get_mask(insert_Ns=False))
+
     def get_mask(self, insert_Ns: bool = True) -> str:
         """Get the mask of the adaptor part.
 
@@ -172,7 +177,9 @@ def get_mask(self, insert_Ns: bool = True) -> str:
             and self.index_seq is None
             and insert_Ns
         ):
-            raise UserWarning("Adaptor has i5 but no sequence was specified")
+            raise UserWarning(
+                f"Can't create mask for adaptor '{self.name}' with unspecified index."
+            )
 
         if self.index_seq is not None or not insert_Ns:
             mask = re.sub(INDEX_TOKEN, "N" * index_mask_length, self.sequence_token)

anglerfish/explore/explore.py

@@ -134,10 +134,7 @@ def run_explore(
                     match_col_df
                 )
 
-                thres = round(
-                    (adaptor_end.len_before_index + adaptor_end.len_after_index)
-                    * good_hit_threshold
-                )
+                thres = round(adaptor_end.len_constant * good_hit_threshold)
                 df_good_hits = df_good_hits[df_good_hits["match_1_len"] >= thres]
 
                 median_insert_length = None