Error with read_meme about universalmotif HOT 5 CLOSED

Hi,

Thanks for trying out the package. I'm glad you find it useful.

Unfortunately I am failing to reproduce your error, though I don't see anything wrong with what you've done. Are your sequences using a custom alphabet? If so read_meme() could be having trouble parsing the motif file.

If you cut down your fasta file to a few hundred sequences, do you still encounter this error? If so, would you be able to upload this sample file for me to test? (Or email it to me directly.)

Alternatively: if you keep the output (via the output argument), can you still trigger the error by using read_meme() on the output motif file? If so, you could send this instead.

Thanks.

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Thanks!

Looks like read_meme() was having trouble parsing the longer amino acid alphabet. I've pushed a patch (v1.3.66) which should fix the issue. Let me know if it works for you.

from universalmotif.

Thanks a lot, bjmt!

I will check and come back to you!

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Closing. Feel free to reopen if there's still a problem.

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