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fix: handle in-frame complex variants in _get_within_cds_effect() #1227

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fix: handle in-frame complex variants in _get_within_cds_effect() #1227

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28 changes: 25 additions & 3 deletions malariagen_data/veff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -444,11 +444,33 @@ def _get_within_cds_effect(ann, base_effect, cds, cdss):
effect = base_effect._replace(effect="CODON_CHANGE", impact="MODERATE")

else:
# TODO in-frame complex variation (MNP + INDEL)
effect = base_effect._replace(
effect="TODO in-frame complex variation (MNP + INDEL)", impact="UNKNOWN"
# in-frame complex variation: multiple ref bases replaced by a
# different number of alt bases, net change a multiple of 3.
# Reading frame is preserved. Apply the same codon-change logic
# used for simple insertions and deletions above.
is_codon_changed = (strand == "+" and ref_aa[0] != alt_aa[0]) or (
strand == "-" and ref_aa[-1] != alt_aa[-1]
)

if len(alt) > len(ref):
if is_codon_changed:
effect = base_effect._replace(
effect="CODON_CHANGE_PLUS_CODON_INSERTION", impact="MODERATE"
)
else:
effect = base_effect._replace(
effect="CODON_INSERTION", impact="MODERATE"
)
else:
if is_codon_changed:
effect = base_effect._replace(
effect="CODON_CHANGE_PLUS_CODON_DELETION", impact="MODERATE"
)
else:
effect = base_effect._replace(
effect="CODON_DELETION", impact="MODERATE"
)

return effect


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