Add reference sequences extracted from a genome FASTA onto a panel BED table

For each BED interval, extracts length bases starting at 0-based start (Biostrings 1-based start + 1) from the contig named in #chrom. Minus- strand intervals are reverse-complemented. Genome FASTA names are truncated at the first whitespace.

Usage

add_ref_seqs_with_full_genome_ref_fasta(
  ref_bed,
  genome_fasta,
  output = NULL,
  overwrite = FALSE
)

Arguments

ref_bed: Path to a panel BED TSV, or a data frame with the same columns. See Inputs.
genome_fasta: Path to a genome FASTA. See Inputs.
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.
genome_fasta: Genome FASTA to extract intervals from.

Outputs

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

Running

add_ref_seqs_with_full_genome_ref_fasta(
  ref_bed = "ref_bed.tsv",
  genome_fasta = "genome.fasta",
  output = "ref_bed_with_seq.tsv"
)

Rscript exec/add_ref_seqs_with_full_genome_ref_fasta \
  --ref_bed ref_bed.tsv \
  --genome_fasta genome.fasta \
  --output ref_bed_with_seq.tsv

Requires Biostrings (Suggests).