fix (bruteForce): accepter variants are skipped if the donor transcri…

…pt has variants with the same coordinate. #810

CHANGELOG.md

@@ -32,6 +32,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 - Fixed `callVariant` with altSplice insertion with intronic frameshift variant which is very closed to the end of the subgraph. #803
 
+- Fixed `bruteForce` that accepter variants are skipped if the donor transcript has variants with the same coordinate. #810
+
 ## [1.2.0] - 2023-08-03
 
 ### Fixed

moPepGen/util/brute_force.py

@@ -1091,47 +1091,47 @@ def translational_modification(self, seq:Seq, lhs:int, tx_lhs:int,
     def generate_variant_comb(self, fusion:bool, circ_rna:bool
             ) -> Iterable[seqvar.VariantRecordPool]:
         """ Generate combination of variants. """
-        variant_type_mapper:Dict[seqvar.VariantRecord, str] = {}
+        variant_type_mapper:Dict[str, Tuple[seqvar.VariantRecord, str]] = {}
         start_index = self.tx_seq.orf.start + 3 if bool(self.tx_seq.orf) else 3
         for variant in self.variant_pool[self.tx_id].transcriptional:
             if variant.location.start == start_index - 1 \
                     and (variant.is_insertion() or variant.is_deletion()) \
                     and not variant.is_alternative_splicing():
                 variant.to_end_inclusion(self.tx_seq)
 
-            variant_type_mapper[variant] = 'transcriptional'
+            variant_type_mapper[variant.id] = (variant, 'transcriptional')
         for variant in self.variant_pool[self.tx_id].intronic:
-            variant_type_mapper[variant] = 'intronic'
+            variant_type_mapper[variant.id] = (variant, 'intronic')
         if fusion:
             for variant in self.variant_pool[self.tx_id].fusion:
                 if variant.location.start < start_index - 1:
                     continue
-                variant_type_mapper[variant] = 'fusion'
+                variant_type_mapper[variant.id] = (variant, 'fusion')
                 accepter_tx_id = variant.attrs['ACCEPTER_TRANSCRIPT_ID']
                 if accepter_tx_id not in self.variant_pool:
                     continue
                 accepter_var_series = self.variant_pool[accepter_tx_id]
                 for accepter_var in accepter_var_series.transcriptional:
-                    variant_type_mapper[accepter_var] = 'transcriptional'
+                    variant_type_mapper[accepter_var.id] = (accepter_var, 'transcriptional')
                 for accepter_var in accepter_var_series.intronic:
-                    variant_type_mapper[accepter_var] = 'intronic'
+                    variant_type_mapper[accepter_var.id] = (accepter_var, 'intronic')
         if circ_rna:
             for variant in self.variant_pool[self.tx_id].circ_rna:
-                variant_type_mapper[variant] = 'circ_rna'
+                variant_type_mapper[variant.id] = (variant, 'circ_rna')
 
-        all_variants = list(variant_type_mapper.keys())
+        all_variants = [v[0] for v in variant_type_mapper.values()]
 
         for i in range(len(all_variants)):
             for inds in combinations(range(len(all_variants)), i + 1):
                 variants = [all_variants[i] for i in inds]
-                if fusion and not any(variant_type_mapper[v] == 'fusion' for v in variants):
+                if fusion and not any(variant_type_mapper[v.id][1] == 'fusion' for v in variants):
                     continue
-                if circ_rna and not any(variant_type_mapper[v] == 'circ_rna' for v in variants):
+                if circ_rna and not any(variant_type_mapper[v.id][1] == 'circ_rna' for v in variants):
                     continue
                 pool = seqvar.VariantRecordPool()
                 pool.anno = self.variant_pool.anno
                 for variant in variants:
-                    var_type = variant_type_mapper[variant]
+                    var_type = variant_type_mapper[variant.id][1]
                     tx_id = variant.transcript_id
                     if var_type == 'transcriptional':
                         pool.add_transcriptional_variant(variant, tx_id)