Merge pull request #73 from alneberg/umi_format_explore_fix

Umi format explore fix

anglerfish/demux/adaptor.py

@@ -90,24 +90,44 @@ def __init__(self, sequence, name, delim, index):
         self.name = name
         self.delim = delim
         self.index = index
+        self.umi_after = 0
+        self.umi_before = 0
+        self.len_after_index = 0
+        self.len_before_index = 0
+
+        # Dynamically assign attributes
+        self.umi = re.findall(udelim, self.sequence)
+
+        # TODO Duplicated from Adaptor class, will be merged later
+        # Check if UMI is before or after index
+        if len(self.umi) > 0 and ">" + self.umi[0] in self.sequence:
+            # The index region is INDEX+UMI
+            self.umi_after = int(re.search(ulen, self.umi[0]).group(1))
+            self.len_before_index = len(idelim.split(self.sequence)[0])
+            self.len_after_index = len(udelim.split(self.sequence)[-1])
+        elif len(self.umi) > 0 and self.umi[0] + "<" in self.sequence:
+            # The index region is UMI+INDEX
+            self.umi_before = int(re.search(ulen, self.umi[0]).group(1))
+            self.len_before_index = len(udelim.split(self.sequence)[0])
+            self.len_after_index = len(idelim.split(self.sequence)[-1])
+        elif len(self.umi) > 0:
+            # TODO give details which adaptor has the problem
+            raise UserWarning(
+                "Found adaptor with UMI but it does not flank an index. This is not supported."
+            )
+        # Non UMI cases
+        elif has_match(idelim, self.sequence):
+            self.len_before_index = len(idelim.split(self.sequence)[0])
+            self.len_after_index = len(idelim.split(self.sequence)[-1])
 
     def has_index(self):
         return self.sequence.find(self.delim) > -1
 
-    def len_before_index(self):
-        return self.sequence.find(self.delim)
+    def len_before_index_region(self):
+        return self.len_before_index
 
-    def len_after_index(self):
-        return len(self.sequence) - self.sequence.find(self.delim) - len(self.delim)
-
-    def get_mask(self, insert_Ns):
-        if self.has_index():
-            if not insert_Ns:
-                return self.sequence.replace(self.delim, "")
-            else:
-                return self.sequence.replace(self.delim, "N" * len(self.index))
-        else:
-            return self.sequence
+    def len_after_index_region(self):
+        return self.len_after_index
 
 
 # General function to check if a string contains a pattern

anglerfish/explore/explore.py

@@ -104,9 +104,11 @@ def run_explore(
 
                 # Alignment thresholds
                 before_thres = round(
-                    adaptor_end.len_before_index() * good_hit_threshold
+                    adaptor_end.len_before_index_region() * good_hit_threshold
+                )
+                after_thres = round(
+                    adaptor_end.len_after_index_region() * good_hit_threshold
                 )
-                after_thres = round(adaptor_end.len_after_index() * good_hit_threshold)
                 insert_thres_low = insert_thres_low
                 insert_thres_high = insert_thres_high
 
@@ -133,7 +135,10 @@ def run_explore(
                 ] = match_col_df
 
                 thres = round(
-                    (adaptor_end.len_before_index() + adaptor_end.len_after_index())
+                    (
+                        adaptor_end.len_before_index_region()
+                        + adaptor_end.len_after_index_region()
+                    )
                     * good_hit_threshold
                 )
                 df_good_hits = df_good_hits[df_good_hits["match_1_len"] >= thres]