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Turn off reverse complements #56

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Turakar opened this issue Dec 2, 2024 · 3 comments · May be fixed by #57
Closed

Turn off reverse complements #56

Turakar opened this issue Dec 2, 2024 · 3 comments · May be fixed by #57

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@Turakar
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Turakar commented Dec 2, 2024

It would be useful if a user could pass revcomp=False to disable reverse complementing for matching. In my use case, reverse complements should not match each other, but be considered separate. Could this be added to the library?

It seems like updating _align_patterns() should be enough?
@jmschrei
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jmschrei commented Dec 2, 2024

Conceptually, it could be done. However, I think this is built-in to many methods, the most important being the seqlet similarity scores, and I don't have the bandwidth to add this feature. Sorry about that.

@jmschrei jmschrei closed this as completed Dec 2, 2024
@Turakar
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Turakar commented Dec 3, 2024

Not considering possible performance improvements - is it wrong to only change _align_patterns()?

@jmschrei
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jmschrei commented Dec 3, 2024

Yeah, you'd need too also change the seqlet similarity score in at least https://github.com/jmschrei/tfmodisco-lite/blob/main/modiscolite/affinitymat.py#L67. I don't remember all the places it would matter -- it's been a while since I've looked at the code.

@Turakar Turakar mentioned this issue Jan 2, 2025
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Make reverse complementing optional Turakar/tfmodisco-lite
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@jmschrei @Turakar