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Merged
Peter-J-Freeman merged 7 commits into from
Jun 1, 2026
Merged

Develop #817

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c81f925
Fixes for Selenon code handling in issue #815 variant NM_020451.3:c_4…
Peter-J-Freeman May 15, 2026
31737d4
Updates to issue #815 to fix dels.
Peter-J-Freeman May 15, 2026
d7530a0
Final fixes for #815, inc. switch to only VV c > p
Peter-J-Freeman May 18, 2026
d0c94c0
Add user info when Selenocysteine might affect Ter
John-F-Wagstaff May 27, 2026
8262c14
Merge new v. of pull request #816 from issue_815v2
John-F-Wagstaff May 30, 2026
b386fa0
slight tweaks to the chrName to ID dicts
Peter-J-Freeman May 26, 2026
ed20322
Add additional Sec inclusion test related to issue #818
Peter-J-Freeman May 26, 2026
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20 changes: 17 additions & 3 deletions VariantValidator/modules/mappers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -759,18 +759,28 @@ def transcripts_to_gene(variant, validator, select_transcripts_dict_plus_version
hgvs_refseq = 'RefSeqGene record not available'

# Predicted effect on protein
logger.info(f"Translating {hgvs_coding} in transcripts_to_gene")
try:
protein_dict = validator.myc_to_p(hgvs_coding, variant.evm, re_to_p=False, hn=variant.hn)
except NotImplementedError as e:
# import traceback
# traceback.print_exc()
logger.info(f"Protein dict creation failed with exception: {str(e)}")
protein_dict = {'hgvs_protein': None, 'error': str(e)}
variant.warnings.append(str(e))
except vvhgvs.exceptions.HGVSDataNotAvailableError as e:
# import traceback
# traceback.print_exc()
logger.info(f"Protein dict creation failed with exception: {str(e)}")
protein_dict = {'hgvs_protein': None, 'error': str(e)}
variant.warnings.append(str(e))
else:
logger.info(f"Protein dict creation successful: {protein_dict}")

if protein_dict['error'] == '':
if protein_dict['error'] == '' or protein_dict['error'].startswith('ProteinTranslationInfo:'):
hgvs_protein = protein_dict['hgvs_protein']
if protein_dict['error']:
variant.warnings.append(protein_dict['error'])
else:
error = protein_dict['error']
if not error.startswith('ProteinTranslationError:' ):
Expand Down Expand Up @@ -829,8 +839,10 @@ def transcripts_to_gene(variant, validator, select_transcripts_dict_plus_version
try:
# Predicted effect on protein
protein_dict = validator.myc_to_p(c_for_p, variant.evm, re_to_p=False, hn=variant.hn)
if protein_dict['error'] == '':
if protein_dict['error'] == '' or protein_dict['error'].startswith('ProteinTranslationInfo:'):
hgvs_protein = protein_dict['hgvs_protein']
if protein_dict['error']:
variant.warnings.append(protein_dict['error'])
else:
error = protein_dict['error']
if error == 'Cannot identify an in-frame Termination codon in the variant mRNA sequence':
Expand All @@ -846,8 +858,10 @@ def transcripts_to_gene(variant, validator, select_transcripts_dict_plus_version
if hgvs_coding.posedit.pos.start.offset == 0 and hgvs_coding.posedit.pos.start.offset == 0 and \
'?' in str(hgvs_protein):
protein_dict = validator.myc_to_p(hgvs_coding, variant.evm, re_to_p=False, hn=variant.hn)
if protein_dict['error'] == '':
if protein_dict['error'] == '' or protein_dict['error'].startswith('ProteinTranslationInfo:'):
hgvs_protein = protein_dict['hgvs_protein']
if protein_dict['error']:
variant.warnings.append(protein_dict['error'])
else:
error = protein_dict['error']
if error == 'Cannot identify an in-frame Termination codon in the variant mRNA sequence':
Expand Down
2 changes: 0 additions & 2 deletions VariantValidator/modules/seq_data.py
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Expand Up @@ -1742,7 +1742,6 @@ def to_accession(chr_num, primary_assembly):
'HSCHR1_6_CTG31': 'NW_025791755.1',
'HG1384_PATCH': 'NW_021159988.1',
'HG2231_HG2496_PATCH': 'NW_025791767.1',
'NW_025791768.1': 'NW_025791768.1',
'HG2052_PATCH' : 'NW_025791766.1',
'HSCHR2_6_CTG1': 'NW_025791763.1',
'HSCHR2_10_CTG7_2': 'NW_025791760.1',
Expand Down Expand Up @@ -3305,7 +3304,6 @@ def to_chr_num_refseq(accession, primary_assembly):
'NW_025791755.1': 'HSCHR1_6_CTG31',
'NW_021159988.1': 'HG1384_PATCH',
'NW_025791767.1': 'HG2231_HG2496_PATCH',
'NW_025791768.1': 'NW_025791768.1',
'NW_025791766.1': 'HG2052_PATCH',
'NW_025791763.1': 'HSCHR2_6_CTG1',
'NW_025791760.1': 'HSCHR2_10_CTG7_2',
Expand Down
2 changes: 2 additions & 0 deletions VariantValidator/modules/utils.py
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Expand Up @@ -294,6 +294,7 @@ def pro_inv_info(prot_ref_seq, prot_var_seq):
"""
Function which predicts the protein effect of c. inversions
"""
logger.info("pro_inv_info function called")
info = {
'variant': 'true',
'prot_del_seq': '',
Expand Down Expand Up @@ -392,6 +393,7 @@ def pro_inv_info(prot_ref_seq, prot_var_seq):


def pro_delins_info(prot_ref_seq, prot_var_seq, in_frame=False):
logger.info(f"pro_delins_info function called")
info = {
'variant': 'true',
'prot_del_seq': '',
Expand Down
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