Dedropy mistakenly looking for DNA alphabet in ProteinCharacterMatrix.get

jeetsukumaran / DendroPy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

https://pypi.org/project/DendroPy/.

BSD 3-Clause "New" or "Revised" License

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Dedropy mistakenly looking for DNA alphabet in ProteinCharacterMatrix.get #81

Closed tauanajc closed 6 months ago

tauanajc commented 7 years ago

When using: dendropy.ProteinCharacterMatrix.get(path="file.nex", schema="nexus") Dendrophy returns an error about DNA alphabet: Error parsing data source 'file.nex' on line 7 at column 14: Unrecognized character state symbol for state alphabet 'DNA' (DnaStateAlphabet) : 'L'

I haven't been able to find a way around this.

jeetsukumaran commented 6 years ago

As might be inferred from the error, it is finding the letter "L" in the sequence data and is not happy about it because L is not a DNA alphabet. Without the data file, that's all that can be said right now.

mmore500 commented 6 months ago

Closing this for now, but if more information can be provided happy to re-open. :+1: