add gene size parameters to CLI

[cjprybol]

#31

Didn't run any tests but I think this is the right place to make the edits

[althonos]

Thanks! Could you just change the flags to be in kebab-case (--min-edge-gene instead of --min_edge_gene)?

[cjprybol]

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 min_gene ( 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

[althonos]

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!