goalign detecting amino acid file as nucleotide file

[frikinzi]

Thank you for developing this helpful tool.

I'm running into an issue with goalign compute where the tool is automatically detecting my file as a nucleotide file even though there are amino acid characters in it (S, Y, T). Below I include a snippet of my .faa file.

>GCA_0
SCYTGAK
>GCA_1
SAYSASK
>GCA_2
SAYSASK
>GCA_3
SAYSASK

The command I ran is: goalign compute pssm -i N85.faa > N85.count.tsv

The output of that command is this, when I would expect there to be amino acid characters.

I tried including --auto-detect, but it didn't fix my problem.

I installed goalign through conda.

Any help would be appreciated. Please let me know if I can provide any other information. Thank you!

[fredericlemoine]

Hi,
Thank you for your suggestion.
I've been thinking of adding this feature for a while. I've just added the option "--alphabet" to goalign commands. It allows to specify the alphabet if you don't want the one that is automatically detected (because of common IUPAC characters). If you have a way to test it, it would be great.
Thanks

[frikinzi]

I just tested it and it worked! Thanks so much for the quick response and fix.