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FePhyFoFum / phyx

phylogenetics tools for linux (and other mostly posix compliant) computers
blackrim.org
GNU General Public License v3.0
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pxtlate detects AA when DNA is present #167

Closed HeatherKates closed 2 years ago

HeatherKates commented 2 years ago

temp.txt

I am getting the error: Error: incorrect alignment type provided. DNA was expected, but AA detected. Exiting.

If I excerpt any single sequence from the fasta, I don't get the error, so I thought it might be related to line breaks or some other character I can't see. I have tried removing whitespace and dos2unix (the text file was written in python, so probably moot). I have also tried shortening and/or removing special characters from the sequence headers. I have translated this alignment using translatorx and that tool runs fine. Any ideas? Could so many NNN's be the issue?

Thanks!

josephwb commented 2 years ago

Thanks for reporting that. It is interpreting the Ns as amino acids, so every character seems to be a valid amino acid. I will fix this. In the meantime, if you replace N with - like this then things will work.

josephwb commented 2 years ago

This should be fixed with 98727b7. Please let me know if this works for you, and close if you are satisfied.