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Uncertain stop codon in protein descriptions (fs and ext)
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
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- mutalyzer/util.py 58 additions, 29 deletionsmutalyzer/util.py
- mutalyzer/variantchecker.py 36 additions, 24 deletionsmutalyzer/variantchecker.py
- tests/data/NM_001199.3.gb.bz2 0 additions, 0 deletionstests/data/NM_001199.3.gb.bz2
- tests/fixtures.py 2 additions, 0 deletionstests/fixtures.py
- tests/test_variantchecker.py 33 additions, 0 deletionstests/test_variantchecker.py
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