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Fix short_description for PrematureStop with empty aa_ref #216

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joaoe opened this issue Mar 15, 2017 · 1 comment
Open

Fix short_description for PrematureStop with empty aa_ref #216

joaoe opened this issue Mar 15, 2017 · 1 comment

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@joaoe
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joaoe commented Mar 15, 2017

Consider the variant chr1 99772782 A ATAA on GRCm38. It produces a annotation on transcript ENSMUST00000086738. The short_descriptionis p.7*.
This seems wrong. It should be p.7ins*. The code in PrematureStop.short_description does not handle empty aa_ref, unlike the code in KnownAminoAcidChange.short_description.

Suggestion: move the code from KnownAminoAcidChange.short_description into a function that accepts the arguments aa_ref,aa_alt,aa_mutation_start_offset. Call that function from both KnownAminoAcidChange and PrematureStopwhere the latter appends the stop codon * to aa_alt.

@joaoe
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joaoe commented Apr 20, 2017

Also, KnownAminoAcidChange.short_description does not add +1 to aa_mutation_start_offset in two cases. Is that correct ?

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