Remove new getattr references

biocommons · Jan 2, 2024 · 444bd03 · 444bd03
1 parent d965a85
commit 444bd03
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Showing 2 changed files with 29 additions and 23 deletions.
diff --git a/src/hgvs/assemblymapper.py b/src/hgvs/assemblymapper.py
@@ -244,22 +244,23 @@ def _alt_ac_for_tx_ac(self, tx_ac):
         return alt_acs[0]
 
     def _replace_reference(self, var):
-        if (getattr(var.posedit.pos.start, 'offset', 0) != 0 or getattr(var.posedit.pos.end, 'offset', 0) != 0):
-            if var.type != 'g':
-                alt_ac = self._alt_ac_for_tx_ac(var.ac)
-                if var.type == 'c':
-                    var_g = super(AssemblyMapper, self).c_to_g(var, alt_ac, alt_aln_method=self.alt_aln_method)
-                if var.type == 'n':
-                    var_g = super(AssemblyMapper, self).n_to_g(var, alt_ac, alt_aln_method=self.alt_aln_method)
-                if var.type == 't':
-                    var_g = super(AssemblyMapper, self).t_to_g(var, alt_ac, alt_aln_method=self.alt_aln_method)
-                super(AssemblyMapper, self)._replace_reference(var_g)
-                ref = var_g.posedit.edit.ref
-                if self._fetch_AlignmentMapper(tx_ac=var.ac).strand == -1:
-                    ref = reverse_complement(ref)
-                var.posedit.edit.ref = ref
-                _logger.debug("Replaced reference sequence in {var} with {ref}".format(var=var, ref=var_g.posedit.edit.ref))
-                return var
+        if (
+            var.type in "cn"
+            and var.posedit.pos is not None
+            and (var.posedit.pos.start.offset != 0 or var.posedit.pos.end.offset != 0)
+        ):
+            alt_ac = self._alt_ac_for_tx_ac(var.ac)
+            if var.type == 'c':
+                var_g = super(AssemblyMapper, self).c_to_g(var, alt_ac, alt_aln_method=self.alt_aln_method)
+            if var.type == 'n':
+                var_g = super(AssemblyMapper, self).n_to_g(var, alt_ac, alt_aln_method=self.alt_aln_method)
+            super(AssemblyMapper, self)._replace_reference(var_g)
+            ref = var_g.posedit.edit.ref
+            if self._fetch_AlignmentMapper(tx_ac=var.ac).strand == -1:
+                ref = reverse_complement(ref)
+            var.posedit.edit.ref = ref
+            _logger.debug("Replaced reference sequence in {var} with {ref}".format(var=var, ref=var_g.posedit.edit.ref))
+            return var
 
         return super(AssemblyMapper, self)._replace_reference(var)
 

diff --git a/src/hgvs/variantmapper.py b/src/hgvs/variantmapper.py
@@ -468,11 +468,13 @@ def _replace_reference(self, var):
             # these types have no reference sequence (zero-width), so return as-is
             return var
 
-        pos = var.posedit.pos
-        if (getattr(pos.start, 'offset', 0) != 0 or getattr(pos.end, 'offset', 0) != 0):
-            if var.type != "g":
-                _logger.info("Can't update reference sequence for intronic variant {}".format(var))
-                return var
+        if (
+            var.type in "cnr"
+            and var.posedit.pos is not None
+            and (var.posedit.pos.start.offset != 0 or var.posedit.pos.end.offset != 0)
+        ):
+            _logger.info("Can't update reference sequence for intronic variant {}".format(var))
+            return var
 
         # For c. variants, we need coords on underlying sequences
         if var.type == "c":
@@ -483,8 +485,11 @@ def _replace_reference(self, var):
         else:
             pos = var.posedit.pos
 
-        seq_start = pos.start.base + getattr(pos.start, 'offset', 0) - 1
-        seq_end = pos.end.base + getattr(pos.end, 'offset', 0)
+        seq_start = pos.start.base - 1
+        seq_end = pos.end.base
+        if var.type in "cnr":
+            seq_start += pos.start.offset
+            seq_end += pos.end.offset
 
         # When strict_bounds is False and an error occurs, return
         # variant as-is