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bvalot / pyMLST

whole genome MLST analysis
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Spelling mistake in recombination sub-command #19

Closed charlie-durant closed 8 months ago

charlie-durant commented 8 months ago

Followed documentation here to perform recombination analysis.

wgMLST recombination -h

This command results in: Error: Unknown sub-command 'recombination'

command that works is wgMLST recombinaison -h

Usage: wgMLST recombinaison [OPTIONS] GENES ALIGNMENT

  Search potential gene re-combinations from wgMLST database export.

Options:
  -o, --output FILENAME  Output number of variations by genes
                         (default:stdout).
  -h, --help             Show this message and exit.
bvalot commented 8 months ago

Hi Charlie,

I'm currently working on 2.1.5 release that corresponds to the publication of pyMLST in Microbials Genomics. For this purpose, I make some spellchecking correction on the program and so in the docs.

Actually, you must use the 2.1.4 version were the command is 'recombinaison' (french word for recombination)

You can check all the command using: wgMLST --help

Sorry for this, I hope upload new version soon.

bvalot commented 8 months ago

I push the 2.1.5 version on pypi. Update your package and normally the command name would be as the documentation

charlie-durant commented 8 months ago

No worries, makes sense! Thanks