Translate loci of interest from microhaplotype sequences

Aligns each unique haplotype to its panel reference with an overlap pairwise alignment, extracts the codon at each locus of interest, and translates it.

Usage

translate_loci_of_interest(
  allele_table,
  ref_bed,
  loci_of_interest,
  output_dir,
  select_target_names = NULL,
  select_specimen_names = NULL,
  overwrite_dir = FALSE,
  output_stop_codons = FALSE,
  collapse_calls_by_summing = FALSE
)

Arguments

allele_table: Path or data frame of allele table. See Inputs.
ref_bed: Path or data frame of panel BED with ref_seq. See Inputs.
loci_of_interest: Path or data frame of codon BED. See Inputs.
output_dir: Directory to write results. Created if missing.
select_target_names: Optional comma-separated names, path to a one-column TSV, or character vector of targets to keep.
select_specimen_names: Optional comma-separated names, path to a one-column TSV, or character vector of specimens to keep.
overwrite_dir: If FALSE (default), refuse to replace an existing output_dir.
output_stop_codons: If FALSE (default), treat * as untranslatable (along with X).
collapse_calls_by_summing: If TRUE, sum reads across overlapping targets; otherwise keep the target with the highest read count.

Value

A named list with loci_of_interest_for_target_for_microhap, amino_acid_calls, collapsed_amino_acid_calls, loci_covered_by_target_samples_info, and untranslatable.

Details

Inputs

allele_table: Allele table (specimen_name, target_name, reads, seq), as a file path or data frame. See vignette("input-formats", package = "PGEcore").
ref_bed: Panel BED with ref_seq (#chrom, start, end, target_name, length, strand, ref_seq).
loci_of_interest: Codon BED (#chrom, start, end, name, length, strand, gene, gene_id, aa_position); each locus must have length == 3.

Outputs

output_dir: Directory receiving loci_of_interest_for_target_for_microhap.tsv.gz, amino_acid_calls.tsv.gz, collapsed_amino_acid_calls.tsv.gz, loci_covered_by_target_samples_info.tsv, and optionally allele_table_out_untranslatable.tsv.

Running

translate_loci_of_interest(
  allele_table = "allele_table.tsv",
  ref_bed = "ref_bed_with_seq.tsv",
  loci_of_interest = "loci.bed",
  output_dir = "translate_out"
)

Rscript exec/translate_loci_of_interest \
  --allele_table allele_table.tsv \
  --ref_bed ref_bed_with_seq.tsv \
  --loci_of_interest loci.bed \
  --output_dir translate_out

Requires Biostrings and pwalign (Suggests).