phyluce_align_remove_locus_name_from_files does not clean names if output is fasta

faircloth-lab / phyluce

software for UCE (and general) phylogenomics

http://phyluce.readthedocs.org/

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phyluce_align_remove_locus_name_from_files does not clean names if output is fasta #341

Closed tauanajc closed 3 weeks ago

tauanajc commented 3 weeks ago

Hi there!

I aligned my UCEs without any trimming and saved as fasta. When using the command to clean the names, it only worked with the default nexus. When I used --output-format fasta, the name was duplicated with one version clean followed by the original separated by a space, like so: Diodora_cayenensis_FMNH281526_gLIB_0098 uce-2172_Diodora_cayenensis_FMNH281526_gLIB_0098 | uce-2172.

brantfaircloth commented 3 weeks ago

That's weird. But, I've fixed the bug in the code that was causing the problem. That fix won't make it into a release for a while, but it's pretty simple if you want to implement on your own. I'm about to reference the issue in a commit and the fix should pop up below.