update 0.0.28

[oclaisse]

Hello, I have installed clinker with conda create -n clinker -c conda-forge -c bioconda clinker-py I have try to update to v0.0.28 because I have some errors when I want to compare some genomes: but it stay on clinker v0.0.26 I don't no if it can solve the below issue: if it due to the size of sequences, or because they are in different contigs, because, I have no problem with phage genomes

"multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/claisse/anaconda3/envs/clinker/lib/python3.11/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) ^^^^^^^^^^^^^^^^^^^ File "/home/claisse/anaconda3/envs/clinker/lib/python3.11/multiprocessing/pool.py", line 51, in starmapstar return list(itertools.starmap(args[0], args[1])) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/claisse/anaconda3/envs/clinker/lib/python3.11/site-packages/clinker/align.py", line 390, in _align_clusters aln = aligner.align(geneA.translation.strip(), ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/claisse/anaconda3/envs/clinker/lib/python3.11/site-packages/Bio/Align/init.py", line 3121, in align score, paths = _aligners.PairwiseAligner.align(self, sA, sB, strand) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: sequence contains letters not in the alphabet

Best regards Olivier

[gamcil]

Hi Olivier, is it possible to upload one of your input files so I can have a look?

[oclaisse]

NRIC649.txt DSM17330.txt Hi Cameron and Happy New Year, here attached two examples files from RAST annotation plateform. I have solved the problem using Prokka .gbf output files. If you can see what is it wrong. And what about the update to v0.0.28

19/01/2023 have you had time to look at the files? and can you help me solve this question?

Sincerely

Olivier

[gamcil]

Hi Olivier, sorry for the delay. It looks like the aligner is getting tripped up by lowercase letters in some protein translations - will add a fix for this in the next release.