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Iteratively replace a k-mer in the genome

Source: R/synth.R
gsynth.replace_kmer.Rd

Performs an iterative replacement of a target k-mer with a replacement sequence. This is useful for creating synthetic genomes with specific motifs removed (e.g., creating a CpG-null genome by iteratively swapping CG to GC).

Usage

gsynth.replace_kmer(
  target,
  replacement,
  output_path = NULL,
  output_format = c("misha", "fasta", "vector"),
  intervals = NULL,
  check_composition = TRUE
)

Arguments

target

The k-mer sequence to remove (e.g., "CG"). Case is ignored.

replacement

The replacement sequence (e.g., "GC"), of the same length as target and different from it (ignoring case). It is written in upper case.

output_path

Path to the output file (ignored when output_format = "vector").

output_format

Output format:

  • "misha": .seq binary format (default)

  • "fasta": FASTA text format

  • "vector": Return sequences as a character vector (does not write to file)

intervals

Genomic intervals to process. If NULL, uses all chromosomes.

check_composition

Logical. If TRUE (default), ensures target and replacement have the same nucleotide composition (preserving exact base counts).

Value

When output_format is "misha" or "fasta", returns invisible NULL and writes to output_path. When output_format is "vector", returns a character vector of modified sequences.

Details

Bubble Sort / Iterative Logic: The function scans the sequence and replaces occurrences of target with replacement. If a replacement creates a new instance of target (e.g., removing "CG" with "GC" in the sequence "CCG" -> "CGC"), the new instance is also replaced. This continues until the sequence is free of the target k-mer.

When target and replacement are permutations of each other (e.g., "CG" and "GC"), this acts as a "bubble sort" of nucleotides, moving bases locally without altering the total GC content or base counts of the genome.

Examples

if (FALSE) { # \dontrun{
# Robust removal of all CpG dinucleotides (preserving GC%)
gsynth.replace_kmer(
    target = "CG",
    replacement = "GC",
    output_path = "genome_no_cpg.seq",
    output_format = "misha"
)
} # }