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PoonLab / ovrf-viz

Review article on overlapping reading frames in viruses
MIT License
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find_ovrfs.py: error at calculating total overlap #7

Closed horaciobam closed 4 years ago

horaciobam commented 5 years ago

In find_ovrfs.py

https://github.com/PoonLab/ovrf-review/blob/3107965a082029c5b83594abe2305ab89521a94a/scripts/find_ovrfs.py#L60-L62

This calculation would mislead the overlap by one nucleotide. Instead we should use:

left = max(l1, l2)
right = min(r1, r2)
overlap = (right - left) + 1
ArtPoon commented 5 years ago

We need to manually check these values:

overlap length string
1 TRATG
2 CATG
4 ATGA