chmod +x make_prg_0.3.0
./make_prg_0.3.0 -h

make_prg -h

$ make_prg --help
usage: make_prg <subcommand> <options>

Subcommand entrypoint

optional arguments:
  -h, --help     show this help message and exit
  -V, --version  show program's version number and exit

Available subcommands:
  
    from_msa     Make PRG from multiple sequence alignment dir
    update       Update PRGs given new sequences output by pandora.

$ make_prg from_msa --help
usage: make_prg from_msa

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input dir: all files in this will try to be read as the supported alignment_format. If not aligned in fasta alignment_format, use -f to input the alignment_format type
  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
                        Output prefix: prefix for the output files
  -t THREADS, --threads THREADS
                        Number of threads
  -f ALIGNMENT_FORMAT, --alignment_format ALIGNMENT_FORMAT
                        Alignment format of MSA, must be a biopython AlignIO input alignment_format. See http://biopython.org/wiki/AlignIO. Default: fasta
  --max_nesting MAX_NESTING
                        Maximum number of levels to use for nesting. Default: 5
  --min_match_length MIN_MATCH_LENGTH
                        Minimum number of consecutive characters which must be identical for a match. Default: 7
  -v, --verbose         Increase output verbosity

$ make_prg update --help
usage: make_prg update

optional arguments:
  -h, --help            show this help message and exit
  -u UPDATE_DS, --update_DS UPDATE_DS
                        Filepath to the update data structures. Should point to a file *.update_DS.
  -d DENOVO_PATHS, --denovo_paths DENOVO_PATHS
                        Filepath containing denovo sequences output by pandora. Should point to a denovo_paths.txt file.
  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
                        Output prefix: prefix for the output files
  -t THREADS, --threads THREADS
                        Number of threads
  --mafft MAFFT         Path to MAFFT executable. By default, it is assumed to be on PATH
  --keep_temp           Keep temp files.
  -v, --verbose         Increase output verbosity