diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c9229b8..f2aaeb9 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -8,6 +8,7 @@ Changelog * Add new submodule ``pychip``. * Add new method :meth:`common.reverse_complement`. * Fix bug in :meth:`common.extract_sequence` where a long DNA sequence output was truncated. +* :issue:`68`: Refresh the variant consequences database from Ensembl VEP. The database's latest update was on May 31, 2021. 0.36.0 (2022-08-12) ------------------- diff --git a/fuc/api/pymaf.py b/fuc/api/pymaf.py index 2d956ee..45f1f1d 100644 --- a/fuc/api/pymaf.py +++ b/fuc/api/pymaf.py @@ -97,7 +97,7 @@ # Below is the list of calculated variant consequences from Ensembl VEP: # https://m.ensembl.org/info/genome/variation/prediction/predicted_data.html -# (accessed on 2021-05-31) +# (accessed on 2023-09-03) # # Note that both frameshift_variant and protein_altering_variant require # additional information to find their correct Variant_Classification. @@ -139,6 +139,11 @@ 'regulatory_region_variant': 'IGR', 'feature_truncation': 'Targeted_Region', 'intergenic_variant': 'IGR', + 'splice_donor_5th_base_variant': 'AMBIGUOUS', + 'splice_donor_region_variant': 'AMBIGUOUS', + 'splice_polypyrimidine_tract_variant': 'AMBIGUOUS', + 'coding_transcript_variant': 'AMBIGUOUS', + 'sequence_variant': 'AMBIGUOUS', } VARCLS_LIST = [