New plugin: ProtVar#818
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jamie-m-a merged 13 commits intoEnsembl:mainfrom Feb 4, 2026
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| $pos-- if $translation_seq =~ /^X/; | ||
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| # we need position of peptide in the ALL_AAS array | ||
| my $peptide_number = ( first_index { $_ eq $peptide } @ALL_AAS ); |
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This is going to return -1 if the AA is X or * or an ambiguous code. Maybe they don't exist in the data? Maybe safer to handle anyway as it'll probably break the next function that uses $peptide_number
| =head1 DESCRIPTION | ||
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| An Ensembl VEP plugin that retrieves data from ProtVar resource providing contexualised information for | ||
| missense variation such destabilization of protein structure, overlapping protein pocket, |
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| missense variation such destabilization of protein structure, overlapping protein pocket, | |
| missense variation such as destabilization of protein structure, overlapping protein pocket, |
| $header{ProtVar_pocket} .= "MpLDDT - Mean pLDDT score of all the residues from AlphaFold2 model used to form the pocket, "; | ||
| $header{ProtVar_pocket} .= "energy - Pocket energy per volume (in kcal/mol unit), "; | ||
| $header{ProtVar_pocket} .= "burriedness - Pocket burriedness (0.0 means entirely exposed and 1.0 means entierly burried), "; | ||
| $header{ProtVar_pocket} .= "RoG - Pocket compactness in terms of radius of gyration (in Angstrom unit), "; |
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| $header{ProtVar_pocket} .= "RoG - Pocket compactness in terms of radius of gyration (in Angstrom unit), "; | |
| $header{ProtVar_pocket} .= "RoG - Pocket compactness in terms of radius of gyration (in Angstroms), "; |
| my %header; | ||
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| if ( defined $self->{stability} ) { | ||
| $header{ProtVar_stability} = "Impact on protein stability in ddG enegry difference."; |
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| $header{ProtVar_stability} = "Impact on protein stability in ddG enegry difference."; | |
| $header{ProtVar_stability} = "Impact on protein stability in ddG energy difference (kcal/mol). Values over 2 are considered likely to be destabilising"; |
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ENSVAR-6378
Test
Example variant
Check the JIRA ticket for example data file for these variant.