Batch Get Sequences with Parallel Processing — batchGetSequences • deepMatchR

Retrieves sequences for multiple alleles in parallel for better performance. Supports both nucleotide and protein sequences.

Usage

batchGetSequences(
  alleles,
  type = c("PROT", "NUC"),
  n_cores = 2,
  use_cache = TRUE,
  cache_dir = NULL,
  verbose = FALSE
)

Arguments

alleles: Character vector of HLA allele names
type: The type of sequence to retrieve. Either "NUC" for nucleotide or "PROT" for protein sequences (default "PROT")
n_cores: Number of cores to use (default: detectCores() - 1)
use_cache: Whether to use caching (default TRUE)
cache_dir: Optional directory for persistent cache
verbose: Logical, whether to print progress messages (default FALSE)

Value

Named list of sequences

Examples

# Get protein sequences for multiple alleles
alleles <- c("A*01:01", "A*02:01", "B*07:02", "B*08:01")
prot_seqs <- batchGetSequences(alleles, type = "PROT")
#> Creating immReferent cache directory at: /home/runner/.immReferent

# Get nucleotide sequences with parallel processing
nuc_seqs <- batchGetSequences(alleles, type = "NUC", n_cores = 4)