fix (bruteForce): MNV combined from two variants located at two adjac…

…ent exons should be excluded for circRNA
uclahs-cds · Oct 27, 2023 · a299f22 · a299f22
1 parent 6362444
commit a299f22
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Showing 4 changed files with 12 additions and 7 deletions.
diff --git a/moPepGen/gtf/GenomicAnnotation.py b/moPepGen/gtf/GenomicAnnotation.py
@@ -255,10 +255,10 @@ def variant_coordinates_to_gene(self, variant:seqvar.VariantRecord,
         ref = variant.ref
         if end_gene - start_gene != end - start:
             if not (variant.type == 'INDEL' and variant.is_deletion()):
-                raise ValueError(f'''
-                    The variant is spanning over at least one entire intron with
-                    the type of '{variant.type}'. Don't know how to handle it.
-                ''')
+                raise ValueError(
+                    'The variant is spanning over at least one entire intron with'
+                    f"the type of '{variant.type}'. Don't know how to handle it."
+                )
             ref = variant.id.split('-')[2]
 
         attrs = copy.copy(variant.attrs)

diff --git a/moPepGen/seqvar/VariantRecordPool.py b/moPepGen/seqvar/VariantRecordPool.py
@@ -204,7 +204,12 @@ def _filter(x):
                 for record in self[tx_id].transcriptional:
                     if record.type in exclude_type:
                         continue
-                    record_gene = self.anno.variant_coordinates_to_gene(record, gene_id)
+                    try:
+                        record_gene = self.anno.variant_coordinates_to_gene(record, gene_id)
+                    except ValueError:
+                        if record.is_merged_mnv():
+                            continue
+                        raise e
                     if _filter(record_gene):
                         if return_coord == 'gene':
                             records.add(record_gene)

diff --git a/moPepGen/svgraph/PeptideVariantGraph.py b/moPepGen/svgraph/PeptideVariantGraph.py
@@ -1226,7 +1226,7 @@ def jsonfy(self):
             variants = set()
             for v in cur.variants:
                 if v.variant.attrs.get('MERGED_MNV'):
-                    variants.update([v.variant.attrs['INDIVIDUAL_VARIANT_IDS']])
+                    variants.update(v.variant.attrs['INDIVIDUAL_VARIANT_IDS'])
                 else:
                     variants.add(v.variant.id)
             node['variants'] = list(variants)

diff --git a/moPepGen/svgraph/ThreeFrameTVG.py b/moPepGen/svgraph/ThreeFrameTVG.py
@@ -1981,7 +1981,7 @@ def jsonfy(self):
             variants = set()
             for v in cur.variants:
                 if v.variant.attrs.get('MERGED_MNV'):
-                    variants.update([v.variant.attrs['INDIVIDUAL_VARIANT_IDS']])
+                    variants.update(v.variant.attrs['INDIVIDUAL_VARIANT_IDS'])
                 else:
                     variants.add(v.variant.id)
             node['variants'] = list(variants)