convert_seq_into_org {avidaR}

Converts a genome instruction sequence into a digital organism file

Description

Converts a genome instruction sequence into a digital organism file.

Usage

convert_seq_into_org(
  genome_seq,
  inst_set = "heads",
  save = FALSE,
  file_name = NULL,
  save_path = getwd(),
  format = "org",
  silent = FALSE
)

Arguments

genome_seq

String of letters.

inst_set

Name of the instruction set. It must be one of the following: heads (default), heads-sex, or transsmt. The names correspond to the instruction set configuration files (e.g., instset-heads.cfg for heads).

save

Logical value (TRUE/FALSE) indicating whether the output should or should not be saved to a file ("FALSE" by default).

file_name

String of characters representing the name of the file without any extension ("organism.org" by default).

save_path

String of characters representing the name of the folder where the digital organism file will be saved.

format

String of characters representing the format of the file ("org" by default).

silent

Logical value (TRUE/FALSE) to show/hide messages ("FALSE" by default).

Value

Data frame. Column names: "instruction".

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

sequence <- get_genome_seq_from_genome_id(
  genome_id = 1,
  triplestore = avidaDB
)$genome_seq[[1]]

convert_seq_into_org(genome_seq = sequence)