Remove new flags on sequence variants

Author: b0d0nne11

src/hgvs/sequencevariant.py

@@ -20,9 +20,6 @@ class SequenceVariant:
     type = attr.ib()
     posedit = attr.ib()
     gene = attr.ib(default=None)
-    shifts_into_exon_and_intron = attr.ib(default=False)
-    is_shifted = attr.ib(default=False)
-    at_boundary = attr.ib(default=False)
 
     def format(self, conf=None):
         """Formatting the stringification of sequence variants

src/hgvs/utils/altseqbuilder.py

@@ -106,7 +106,6 @@ def __init__(self, var_c, transcript_data, translation_table=TranslationTable.st
         # check reference for special characteristics
         self._ref_has_multiple_stops = self._transcript_data.aa_sequence.count("*") > 1
         self._translation_table = translation_table
-        self.at_boundary = False
 
     def build_altseq(self):
         """given a variant and a sequence, incorporate the variant and return the new sequence
@@ -205,38 +204,32 @@ def get_variant_region(self):
             and self._var_c.posedit.pos.start.base in self._transcript_data.exon_start_positions
             and self._var_c.posedit.pos.start.offset == 0
         ):
-            self.at_boundary = True
             result = self.INTRON if global_config.mapping.ins_at_boundary_is_intronic else self.EXON
         elif (
             self._var_c.posedit.edit.type == "dup"
             and self._var_c.posedit.pos.end.base in self._transcript_data.exon_end_positions
             and self._var_c.posedit.pos.end.offset == 0
         ):
-            self.at_boundary = True
             result = self.INTRON if global_config.mapping.ins_at_boundary_is_intronic else self.EXON
         elif (
             self._var_c.posedit.edit.type == "ins"
             and self._var_c.posedit.pos.start.offset == -1 and self._var_c.posedit.pos.end.offset == 0
         ):
-            self.at_boundary = True
             result = self.INTRON if global_config.mapping.ins_at_boundary_is_intronic else self.EXON
         elif (
             self._var_c.posedit.edit.type == "ins"
             and self._var_c.posedit.pos.start.offset == 0 and self._var_c.posedit.pos.end.offset == 1
         ):
-            self.at_boundary = True
             result = self.INTRON if global_config.mapping.ins_at_boundary_is_intronic else self.EXON
         elif (
             self._var_c.posedit.edit.type == "dup"
             and self._var_c.posedit.pos.end.offset == -1
         ):
-            self.at_boundary = True
             result = self.INTRON if global_config.mapping.ins_at_boundary_is_intronic else self.EXON
         elif (
             self._var_c.posedit.edit.type == "dup"
             and self._var_c.posedit.pos.start.offset == 1
         ):
-            self.at_boundary = True
             result = self.INTRON if global_config.mapping.ins_at_boundary_is_intronic else self.EXON
         elif self._var_c.posedit.pos.start.offset != 0 or self._var_c.posedit.pos.end.offset != 0:
             # leave out anything else intronic for now

src/hgvs/variantmapper.py

@@ -445,8 +445,6 @@ def c_to_p(self, var_c, pro_ac=None, alt_ac=None, alt_aln_method=hgvs.global_con
 
         # attempt to shift ins/dup variants from the intron into the exon or vice versa
         if self.shift_over_boundary:
-            shifts_into_exon_and_intron = False
-            is_shifted = False
             original_region = builder.get_variant_region()
             if (
                 var_c.posedit.edit.type in ['ins', 'dup']
@@ -462,10 +460,8 @@ def c_to_p(self, var_c, pro_ac=None, alt_ac=None, alt_aln_method=hgvs.global_con
                         continue
                     if original_region != shifted_region:
                         # a shift is posible
-                        shifts_into_exon_and_intron = True
                         if self.shift_over_boundary_preference.name.lower() == shifted_region:
                             # and that shift is preferred
-                            is_shifted = True
                             reference_data = shifted_reference_data
                             builder = shifted_builder
                         break
@@ -485,10 +481,6 @@ def c_to_p(self, var_c, pro_ac=None, alt_ac=None, alt_aln_method=hgvs.global_con
 
         if self.add_gene_symbol:
             self._update_gene_symbol(var_p, var_c.gene)
-        var_p.at_boundary = builder.at_boundary
-        if self.shift_over_boundary:
-            var_p.shifts_into_exon_and_intron = shifts_into_exon_and_intron
-            var_p.is_shifted = is_shifted
 
         return var_p
 

tests/issues/test_714.py

@@ -7,97 +7,69 @@
         "var_c": "NM_004119.2:c.1837+21_1837+22insCGAGAGAATATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAATTTAGAGTTTGGTAAGAATGGAATGTGCCAAA",
         "exonic":{
             "var_p": "NP_004110.2:p.(Lys614_Val615insAsnGlyMetCysGlnThrArgGluTyrGluTyrAspLeuLysTrpGluPheProArgGluAsnLeuGluPheGlyLys)",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": True,
         },
         "intronic": {
             "var_p": "NP_004110.2:p.?",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": False,
         },
     },
     {
         "name": "dup with splice region preserved",
         "var_c": "NM_004119.2:c.1835_1837+3dup",
         "exonic":{
             "var_p": "NP_004110.2:p.(Gly613_Lys614insIleGly)",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": True,
         },
         "intronic": {
             "var_p": "NP_004110.2:p.?",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": False,
         },
     },
     {
         "name": "dup with splice region preserved",
         "var_c": "NM_005228.4:c.2284-5_2290dup",
         "exonic":{
             "var_p": "NP_005219.2:p.(Ala763_Tyr764insPheGlnGluAla)",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": True,
         },
         "intronic": {
             "var_p": "NP_005219.2:p.?",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": False,
         },
     },
     {
         "name": "dup with splice region preserved",
         "var_c": "NM_004456.4:c.2196-1_2196dup",
         "exonic":{
             "var_p": "NP_004447.2:p.(Tyr733AspfsTer8)",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": True,
         },
         "intronic": {
             "var_p": "NP_004447.2:p.?",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": False,
         },
     },
     {
         "name": "dup with splice region preserved",
         "var_c": "NM_016222.3:c.27+2_27+5dup",
         "exonic":{
             "var_p": "NP_057306.2:p.(Arg10ValfsTer20)",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": True,
         },
         "intronic": {
             "var_p": "NP_057306.2:p.?",
-            "shifts_into_exon_and_intron": True,
-            "is_shifted": False,
         },
     },
     {
         "name": "dup with splice region preserved",
         "var_c": "NM_182758.2:c.2953-31_2953-26dup",
         "exonic":{
             "var_p": "NP_877435.2:p.?",
-            "shifts_into_exon_and_intron": False,
-            "is_shifted": False,
         },
         "intronic": {
             "var_p": "NP_877435.2:p.?",
-            "shifts_into_exon_and_intron": False,
-            "is_shifted": False,
         },
     },
     {
         "name": "dup with broken cigar mapping",
         "var_c": "NM_000267.3:c.8315-290_8457dup",
         "exonic":{
             "var_p": "NP_000258.1:p.?",
-            "shifts_into_exon_and_intron": False,
-            "is_shifted": False,
         },
         "intronic": {
             "var_p": "NP_000258.1:p.?",
-            "shifts_into_exon_and_intron": False,
-            "is_shifted": False,
         },
     }
 ]
@@ -111,13 +83,9 @@ def test_real_c_to_p(case, parser, am37):
     var_c = parser.parse(case["var_c"])
     var_p = am37.c_to_p(var_c)
     assert str(var_p) == case["exonic"]["var_p"]
-    assert var_p.shifts_into_exon_and_intron == case["exonic"]["shifts_into_exon_and_intron"]
-    assert var_p.is_shifted == case["exonic"]["is_shifted"]
 
     am37.shift_over_boundary_preference = ShiftOverBoundaryPreference.INTRON
 
     var_c = parser.parse(case["var_c"])
     var_p = am37.c_to_p(var_c)
     assert str(var_p) == case["intronic"]["var_p"]
-    assert var_p.shifts_into_exon_and_intron == case["intronic"]["shifts_into_exon_and_intron"]
-    assert var_p.is_shifted == case["intronic"]["is_shifted"]