-
Vermaat authored
When a variant results in a frame shift or extension and we don't see a new stop codon in the RNA, the protein description should use the notation for an uncertain stop codon, e.g., `p.(Gln730Profs*?)` instead of `p.(Gln730Profs*96)` where 96 is just the last codon in our transcript [1]. To detect this, we now use `to_stop=False` in our `.translate()` calls, since that will explicitely return `*` characters for stop codons. We also slightly fix the coloring of changes in the protein sequence where previously changed stop codon characters where not included. [1] http://www.hgvs.org/mutnomen/FAQ.html#nostop
Vermaat authoredWhen a variant results in a frame shift or extension and we don't see a new stop codon in the RNA, the protein description should use the notation for an uncertain stop codon, e.g., `p.(Gln730Profs*?)` instead of `p.(Gln730Profs*96)` where 96 is just the last codon in our transcript [1]. To detect this, we now use `to_stop=False` in our `.translate()` calls, since that will explicitely return `*` characters for stop codons. We also slightly fix the coloring of changes in the protein sequence where previously changed stop codon characters where not included. [1] http://www.hgvs.org/mutnomen/FAQ.html#nostop