File naming (.cons.taxonomy)

System Info:

  • MacBook Pro (M1 Pro)
  • OSX Ventura (13.0)
  • Mothur v.1.48.0

Issue: running sub.sample(constaxonomy=xxx.cons.taxonomy) outputs a file named xxx.cons.subsample.taxonomy on Mac OSX (Monterey, Ventura).

Hard to tell if this is a bug or expected behavior - perhaps partially due to a lack of documentation.

constaxonomy is noted as one of the file types used by mothur (constaxonomy file), but the extension for this file type is not listed in the wiki. Commands yield .cons.taxonomy files, but the UTI convention used by Macs since OSX 10.4 prohibits use of dot characters within file extensions. On a Mac, .cons gets interpreted as part of the file name rather than the extension. Is this the expected behavior, where .cons is a prefix added to a .taxonomy file? Seems like they should be distinct file types based on the formatting on .cons.taxonomy files and .taxonomy files.

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This is the subsampled cons.taxonomy file


Thanks for reporting this issue. I have corrected the file extension and the change will be part of our next release.