Command-line arguments and Configuration parameters¶

Parameters can either be provided on the command-line, or specified in a configuration file. If a configuration file is used, the only mandatory command-line argument is --config-file (described here). Otherwise, all Mandatory parameters must be provided.

The following command is an example of using command-line arguments:

python -u -m genonets.sample.minimal --alphabet=DNA --include-indels --input-file=input.csv --tau=0.35 --output-path=results --verbose

Mandatory parameters¶

--config-file: The complete path to the Configuration file.

When specified, all other arguments are treated as optional. Any other arguments provided in addition to this will override the values provided in the configuration file. It is sufficient to provide all other arguments in the configuration file, significantly simplifying the command-line.
--input-file: The complete path to the input file, relative to the current directory. The file must be in the Genonets input-file format.
--output-path: Path to the directory where output files should be generated. The directory will be created if it does not already exist.
--alphabet: Each genotype in the input file must be a string of letters from the alphabet specified here. Available options are RNA, DNA, Protein, and Binary.

tau: Minimum score threshold: all genotypes in the input file with Score values below this threshold will be ignored. Tau must be a number.

Optional parameters¶

--include-indels: If specified, mutations that shift the entire genotype sequence by one letter are also considered. Only point mutations are considered otherwise.

Please note that when used on the command-line, this parameter does not require a value; merely specifying it is sufficient.
--use-reverse-complements: When specified, reverse complements are considered during creation and analysis of genotype networks for alphabet type DNA. This option is not valid for other alphabet types.

Please note that when used on the command-line, this parameter does not require a value; merely specifying it is sufficient.

--store-epistasis-squares: If this parameter is specified and epistasis analysis is requested, all computed squares are stored on disk.

Please note that when used on the command-line, this parameter does not require a value; merely specifying it is sufficient.

--use-all-components: If specified, evolvability analysis considers all connected components, not just the dominant network. It is currently not possible to consider all connected components for analyses other than evolvability.

Please note that when used on the command-line, this parameter does not require a value; merely specifying it is sufficient.
--num-processes: No. of processes to be used in parallel processing. The value must be a positive integer.
--verbose: Information about processing steps is written to stdout.

Please note that when used on the command-line, this parameter does not require a value; merely specifying it is sufficient.
--genetic-code-file: Complete path to the file which contains the mapping from the genetic code to each letter in the selected alphabet. See Custom genetic code for information about the file format.
--codon-alphabet: Alphabet to use for the codons in the genetic code file. The possible values are DNA and RNA.
--include-indels-for-codons: When specified, indels are considered when checking for mutations in codons (for custom genetic code).
--use-rc-for-codons: When specified, reverse complements are considered when checking for mutations in codons. This is only applicable when the alphabet for codons is DNA, and a genetic code file is specified.

Configuration file¶

In order to simplify the command-line, all command-line arguments can be loaded from a configuration file. E.g.,

python -u -m genonets.sample.minimal -c config.cfg

The above command will load all command-line arguments from config.cfg.

Following is a sample config.cfg:

[General]
input-file: input.csv
output-path: results/minimal
alphabet: DNA
tau: 0.35
include-indels: yes
use-reverse-complements: no
store-epistasis-squares: no
use-all-components: no
num-processes: 1
verbose: yes

[Genetic Code]
genetic-code-file: non_standard_code.csv
codon-alphabet: DNA
include-indels-for-codons: no
use-rc-for-codons: no

Please note that the Genetic Code section is optional; it can either be removed or commented out. Placing the # character at the beginning of a line comments it out.