Command Line Options

Input/Output and Execution Options

List of all arguments related to input/output and general execution of the program.

  • -h, --help

    Show help messages for VaxPress and exit.

Input/Output Options

Required Arguments

  • -i FILE, --input FILE

    Path to the input FASTA file containing the CDS or protein sequence.

  • -o DIR, --output DIR

    Path to the output directory.

Optional Arguments

  • --protein

    Input is a protein sequence.

  • --overwrite

    Overwrite output directory if it already exists.

  • -q, --quiet

    Do not print progress messages to stdout.

  • --print-top N

    Print evaluation results of top N sequences at the ends of iterations (default: 10).

  • --report-interval MIN

    Interval of report updates in minutes. In other words, report.html will be updated by this time interval (default: 5).

  • --version

    Show program’s version number and exit.

Execution Options

  • -p N, --processes N

    Number of processes to use (default: 4).

  • --preset FILE

    Use pre-defined options stored in FILE, which has the same format and content as the parameters.json file generated by a VaxPress run. Any options specified in the command line will supersede these preset values.

    Example command to use a preset file:

    vaxpress -i spike.fa -o output \
         --preset parameters.json

    Refer to Using preset values for more information.

  • --addon FILE

    Load a custom fitness function.

    Example command to use a custom fitness function:

    vaxpress -i input.fa -o output_dir \
         --iterations 1000 -p 36 \
         --addon myfunction.py

    Please refer to the Adding a custom scoring function section of this documentation for detailed instructions on using a custom fitness function.

  • --seed NUMBER

    Alter the random seed NUMBER to generate a different sequence under the same settings (default: 922).

  • --folding-engine NAME

    RNA folding engine: vienna or linearfold (default: vienna). linearfold is only available when a separate Python package, linearfold-unofficial, is installed.

  • --default-off

    Disable all fitness functions by default. This is useful when you wish to activate only a select few fitness functions.

Optimization Options

The following is a list of parameters related to the program’s optimization processes. Refer to the Tuning Optimization Parameters section for examples demonstrating the impact of each parameter on the optimization process.

  • --random-initialization

    Randomize all codon selections at the beginning (default: not set).

  • --conservative-start ITER[:WIDTH]

    Mutate the codon selections for the initial WIDTH amino acids only during the first ITER iterations. It is particularly useful when the input sequence is partially optimized, like when it’s generated by LinearDesign. By default, ITER and WIDTH are set to 0 and 7, respectively.

    # Example command line to use --conservative-start option
vaxpress -i spike.fa -o output \
         --iterations 1000 \
         --lineardesign 1 \
         --conservative-start 10:7

  • --iterations N

    Number of iterations (default: 10). See How VaxPress Works to understand how this parameter affect the optimization process.

  • --population N

    Population size to generate every iteration (default: 20).

  • --survivors N

    Number of survivors to pass to the next iteration (default: 2).

  • --initial-mutation-rate RATE

    Initial mutation rate (default: 0.1).

  • --full-scan-interval N

    Number of iterations between full scans of single mutations of unpaired bases (default: 300).

  • --winddown-trigger N

    Decrease the mutation rate if there’s no improvement in the best fitness score for N iterations (default: 15). For a comprehensive explanation, please refer to Adaptive Decrement of Mutation Rate.

  • --winddown-rate RATE

    The mutation rate multiplier that controls the mutation rate when the best fitness score stagnates. The default value is 0.9. For a comprehensive explanation, please refer to the section labeled Adaptive Decrement of Mutation Rate.

  • --boost-loop-mutations WEIGHT[:START]

    Increase the weight of mutations in loop regions by a factor of WEIGHT compared to stem regions. This amplification does not affect the initial part of the sequence preceding START, reducing the influence of the unstructured region near the start codon. The default settings are 1.5:15.

  • --species NAME

    Target species (default: human).

  • --codon-table NAME

    Codon table to identify synonymous codons (default: standard). Codon tables are imported from Bio.Data.CodonTable module. To check for the full list of supported codon tables, please refer to BioPython source code.