CLI Reference¶

The output of the --help commands for the various Freqgen CLI tools is included below for reference.

To summarize the relationship between the different commands, here’s a graph of the commands, the file types they take, and how they relate:

Overview¶

$ freqgen --help
Usage: freqgen [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  generate*  Generate a new DNA sequence with matching...
  aa         Generate an amino acid sequence from FASTA
  featurize  Featurize a FASTA file
  visualize  Visualize the results of an optimization

Generation Reference¶

$ freqgen generate --help
Usage: freqgen generate [OPTIONS]

  Generate a new DNA sequence with matching features

Options:
  -s, --original PATH         The target amino acid sequence.  [required]
  -t, --target PATH           The target frequencies.  [required]
  -v, --verbose               Whether to show optimization progress. Defaults
                              to false.
  -i INTEGER                  How many generations to stop after no
                              improvement. Defaults to 50.
  -p INTEGER                  Population size. Defaults to 100.
  -m FLOAT                    Mutation rate. Defaults to 0.3.
  -c FLOAT                    Crossover rate. Defaults to 0.8.
  -r FLOAT                    Relative improvement threshold. Defaults to 0.0.
  -g, --genetic-code INTEGER  The translation table to use. Defaults to 11,
                              the standard genetic code.
  -o, --output PATH           The path to the output FASTA file.
  --mode [JSD|ED]             The fitness function to use. Defaults to
                              Euclidean distance.
  --help                      Show this message and exit.

Amino Acid Generation Reference¶

$ freqgen aa --help
Usage: freqgen aa [OPTIONS] FILEPATH

  Generate an amino acid sequence from FASTA

Options:
  --mode [freq|seq]           Whether to use the exact AA seq or its
                              frequencies. Defaults to freq.
  -g, --genetic-code INTEGER  The translation table to use. Defaults to 11,
                              the standard genetic code.
  -l, --length INTEGER        The length of the AA sequence (excluding stop
                              codon) to generate if --mode=freq.
  -s, --stop-codon            Whether to include a stop codon. Defaults to
                              true.
  -v, --verbose               Whether to print final result if outputting to
                              file. Defaults to false.
  -o, --output PATH           The output FASTA file.
  --help                      Show this message and exit.

Sequence Featurization Reference¶

$ freqgen featurize --help
Usage: freqgen featurize [OPTIONS] FILEPATH

  Featurize a FASTA file

Options:
  -k INTEGER         Values of k to featurize the seqs for. May be repeated.
  -c, --codon-usage  Whether to include a codon frequency featurization.
  -o, --output PATH  The output YAML file.
  --help             Show this message and exit.

Result Visualization Reference¶

$ freqgen visualize --help
Usage: freqgen visualize [OPTIONS]

  Visualize the results of an optimization

Options:
  -s, --original PATH         The original DNA sequence.
  -t, --target PATH           The target frequencies.  [required]
  -r, --optimized PATH        The optimized DNA sequence.  [required]
  -l, --title TEXT            The title for the graph.
  -w, --width INTEGER         The width of the output graph. Defaults to 1200.
  -h, --height INTEGER        The height of the output graph. Defaults to 400.
  -o, --output PATH           The path to the output HTML file. Defaults to
                              freqgen.html.
  --show / --no-show          Whether to show the resulting visualization
                              file.
  -g, --genetic-code INTEGER  The translation table to use. Defaults to 11,
                              the standard genetic code.
  --help                      Show this message and exit.

Freqgen