Adding aa_ref argument to StopLoss for variants which delete codons before stop #203
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iskandr
changed the title
| @@ -617,14 +617,24 @@ def __init__( | |||
| self, | |||
| variant, | |||
| transcript, | |||
| extended_protein_sequence): | |||
| aa_mutation_start_offset = len(transcript.protein_sequence) | |||
| extended_protein_sequence, | |||
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To keep it in syc with the other classes, perhaps having aa_ref/aa_alt in that order would make more sense.
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Good idea, what do you think of the current changes? I'm a little nervous about having '*' in the aa_ref sequence since the stop codon isn't made explicit anywhere else (e.g. it's not in truncating effects).
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First time I saw "*" in aa_ref I was like "what just crashed my script?" (handling a big vcf file, generating mutated protein sequences to a file).
I don't think it's necessary to have the stop codon there, since it's implied that StopLoss already affects it.
Being pedantic if you have a variant that affects both sides of the stop codon (e.g. chr1 100484693 TTCATCTGAACT CCCTAACCCCCC), then aa_ref would be FI*T.
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Yeah, I agree that it's unnecessary, going to limit the aa_ref/aa_alt sequences to everything before a stop codon.
…ffects required '*' in aa_ref
iskandr
changed the title
Issue: #202
This change is