DNA_ALPHABET does not include IUPAC symbols

[ArtPoon]

https://github.com/PoonLab/OpenRDP/blob/d5cb63962586120b65f22ba7d5d2345969e24517/openrdp/__init__.py#L29

This can cause problems because sequences with mixtures (e.g., N or R) will cause the program to exit! https://github.com/PoonLab/OpenRDP/blob/d5cb63962586120b65f22ba7d5d2345969e24517/openrdp/__init__.py#L315-L316

[ArtPoon]

Things might be more complicated than this - do any of the RDP methods reject sequences with mixtures?

[darrenpmartin]

If you're going tp do something to handle symbols other than ATGC- you should probably write separate versions of the main triplet scanning loops to do this - handling these in the inner loop will be very expensive.

On Wed, Feb 8, 2023 at 5:27 AM Art Poon @.***> wrote:

Things might be more complicated than this - do any of the RDP methods reject sequences with mixtures?

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[ArtPoon]

Should be a simple modification of this function: https://github.com/PoonLab/OpenRDP/blob/d5cb63962586120b65f22ba7d5d2345969e24517/openrdp/common.py#L46-L52

Have not yet found where characters - and * are being handled.

[ArtPoon]

Mixtures can be resolved or averaged at a pre-processing step, before looping over triplets.

[ArtPoon]

I just noticed that the test statement in __init__.py uses an and instead of an or, so it is letting through sequences that contain invalid characters anyhow!