Process Dorado poly(A) signal files for non-A prediction and tail chunk extraction

This function takes a set of Dorado poly(A) signal files (RDS format), extracts features, segments tails, generates Gramian Angular Fields (GAFs), applies classification models to predict non-A residues, and saves both prediction results and tail chunk lists as RDS files in specified output directories. Progress is logged using a cli logging function. This function is not intended to be used outside the pipeline wrapper.

Usage

process_dorado_signal_files(
  polya_signal_files,
  nonA_temp_dir,
  polya_chunks_dir,
  num_cores,
  cli_log
)

Arguments

polya_signal_files

Character vector of paths to poly(A) signal files (RDS format) generated from Dorado outputs.

nonA_temp_dir

Character path to the directory where non-A prediction results will be written. Directory will be created if it does not exist.

polya_chunks_dir

Character path to the directory where tail chunk list RDS files will be written. Directory will be created if it does not exist.

num_cores

Integer number of CPU cores to use for parallel feature extraction and downstream computations.

cli_log

Function used for logging messages.

Value

An (invisible) list summarizing processing results for each input file. Each element contains:

• success (logical): whether the file was processed successfully

• file (character): path to the non-A prediction RDS file if successful

• chunks_file (character): path to the tail chunk list RDS file if successful

• error (character): error message if processing failed

Examples

if (FALSE) { # \dontrun{
# Example usage
signal_files <- list.files("signals/", pattern = "polya_signal.*\\.rds$", full.names = TRUE)
results <- process_dorado_signal_files(
  polya_signal_files = signal_files,
  nonA_temp_dir = "nonA_predictions/",
  polya_chunks_dir = "tail_chunks/",
  num_cores = 4,
  cli_log = function(msg, level, ...) message(sprintf("[%s] %s", level, msg))
)
} # }