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torognes / vsearch

Versatile open-source tool for microbiome analysis
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drop in replacement for usearch #484

Closed lskatz closed 2 years ago

lskatz commented 2 years ago

Hi, thank you for this software. Assuming that everything I want to do in usearch is in vsearch, can I literally rename it? Like mv vsearch usearch? I didn't see that explicitly in the documentation but maybe I missed it. Thank you!

torognes commented 2 years ago

I do not think that is a good idea. It implements most functions in usearch version 7, but not everything is exactly similar. Many functions implemented in later versions of usearch is missing in vsearch. We have tried to make it similar and compatible, but not to the extent that I would recommend literarily replacing it.

lskatz commented 2 years ago

I think this is the line where I want to drop in a replacement, in a 3rd party software. Any tips are appreciated if you have them. Basically I cannot get usearch when building a container for this software and I want to be able to drop in vsearch somehow. https://github.com/zheminzhou/EToKi/blob/1.2/modules/MLSType.py#L181

lskatz commented 2 years ago

I think I figured it out and that I had to switch it to the nt fasta files instead of aa.

torognes commented 2 years ago

Yes, vsearch does not work with amino acid sequences. Those functions of usearch are not implemented.