Closed cjprybol closed 1 year ago
Do you have any preferences for short-hand CLI flags? These are not in the prodigal CLI so there's no existing reference to work off of, but I also struggled to think of any obvious one-letter choices and skipped them so far.
-o
, -m
and -g
are already taken, but something like -l
for mingene ( L ength), -e
for min e dge gene, and/or -p
for overla p_ could work?
I almost always default to long-form myself for clarity so I'm indifferent - happy to go with whatever you prefer!
I also think we're good with the arg parsing and referencing. I initially switched to use the var(args)['argument-name-here']
format but looks like it will auto-replace dashes with underscores so I left the argument passing as is
I also think we're good with the arg parsing and referencing. I initially switched to use the var(args)['argument-name-here'] format but looks like it will auto-replace dashes with underscores so I left the argument passing as is
Yes exactly, that's why I asked about the kebab case, since argparse
already handles the conversion!
Do you have any preferences for short-hand CLI flags? These are not in the prodigal CLI so there's no existing reference to work off of, but I also struggled to think of any obvious one-letter choices and skipped them so far.
I'm fine not having a shortcut, since these are not standard Prodigal arguments, it makes sense to write them out in long-form!
https://github.com/althonos/pyrodigal/issues/31
Didn't run any tests but I think this is the right place to make the edits