Add reference sequences from a targeted FASTA onto a panel BED table

Joins ref_seq onto a panel location table by matching FASTA record names to target_name.

Usage

add_ref_seqs_with_targeted_ref_fasta(
  ref_bed,
  target_fasta,
  output = NULL,
  overwrite = FALSE
)

Arguments

ref_bed

Path to a panel BED TSV, or a data frame with the same columns. See Inputs.

target_fasta

Path to a FASTA whose record names match target_name.

output

Optional output TSV path.

overwrite

If FALSE (default), refuse to overwrite output.

Value

A tibble of ref_bed with a ref_seq column.

Details

Inputs

• ref_bed: Panel BED TSV with header (#chrom, start, end, target_name, length, strand), as a file path or data frame.

• target_fasta: FASTA whose record names match target_name.

Outputs

• output (optional): ref_bed TSV with a ref_seq column. If NULL, results are returned without writing.

Running

add_ref_seqs_with_targeted_ref_fasta(
  ref_bed = "ref_bed.tsv",
  target_fasta = "targets.fasta",
  output = "ref_bed_with_seq.tsv"
)

Rscript exec/add_ref_seqs_with_targeted_ref_fasta \
  --ref_bed ref_bed.tsv \
  --target_fasta targets.fasta \
  --output ref_bed_with_seq.tsv

Requires Biostrings (Suggests) to read the FASTA.

See also

vignette("input-formats", package = "PGEcore")