Load proteins from multiple assemblies — load_proteins • paneffectR

Main entry point for loading protein data. Discovers and loads FASTA files, optionally with associated score and name mapping files.

Usage

load_proteins(
  fasta_dir,
  score_dir = NULL,
  pattern = "*.faa",
  name_mapping = TRUE
)

Arguments

fasta_dir: Character. Directory containing FASTA files.
score_dir: Character. Optional directory containing score CSV files.
pattern: Character. Glob pattern for FASTA files (default: "*.faa").
name_mapping: Logical. Whether to load name mapping files.

Value

A protein_collection object.

Examples

if (FALSE) { # \dontrun{
# Load from omnieff output
proteins <- load_proteins(
  fasta_dir = "reformatted/",
  score_dir = "scored/"
)

# Load just FASTAs
proteins <- load_proteins(fasta_dir = "my_fastas/")
} # }