min_gene option in CLI

[cjprybol]

Hi @althonos,

Thanks for developing this and making it available to others!

Is it possible to utilize the custom gene size threshold via the CLI?

I see the option available for the python API here but I don't think I'm seeing a matching option for the command line help

$ pyrodigal --help
usage: pyrodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type] [-g tr_table] -i input_file [-m] [-n] [-o output_file] [-p mode] [-s start_file] [-t training_file] [-h] [-V]

optional arguments:
  -a trans_file     Write protein translations to the selected file.
  -c                Closed ends. Do not allow genes to run off edges.
  -d nuc_file       Write nucleotide sequences of genes to the selected file.
  -f output_type    Select output format.
  -g tr_table       Specify a translation table to use.
  -i input_file     Specify FASTA input file.
  -m                Treat runs of N as masked sequence; don't build genes across them.
  -n                Bypass Shine-Dalgarno trainer and force a full motif scan.
  -o output_file    Specify output file.
  -p mode           Select procedure.
  -s start_file     Write all potential genes (with scores) to the selected file.
  -t training_file  Write a training file (if none exists); otherwise, read and use the specified training file.
  -h, --help        Show this help message and exit.
  -V, --version     Show version number and exit.

$ pyrodigal -V
pyrodigal v2.0.4

[althonos]

Hi @cjprybol

There is no CLI flag to date because I've been mostly concerned about replicating the Prodigal CLI, but if that would be of interest to you they I'd gladly accept a PR to add a flag for this parameter!

[cjprybol]

Thanks for your help getting these added!

[althonos]

No problem! I'll make a new release ASAP.