Encode/decode DNA sequences

Encode/decode DNA sequences using 2 bits per base for efficient storage, comparison and processing.

Usage

pack_2bits(seq)

unpack_2bits(packed, k)

Arguments

seq

A character vector of DNA sequences (e.g., "ACGT", "GCAT"). Sequences can only contain A, C, G, or T. All sequences must be of the same length.

packed

A 64-bit integer (class integer64) or character representing the packed DNA sequence.

k

Integer. The number of bases in the original DNA sequence.

Value

• pack_2bits: A vector of class integer64 representing the 2-bit packed sequences.

• unpack_2bits: A character string of DNA bases (e.g., "ACGT").

Details

pack_2bits:
Converts DNA strings (containing only A, C, G, T) into a 64-bit integers using 2 bits per base. This allows compact storage and efficient comparison of short DNA sequences (kmers).

unpack_2bits:
Given a 64-bit integer encoding a DNA sequence using 2 bits per base (as from pack_2bits), this function reconstructs the original DNA string.

Examples

# Pack sequence
packed <- pack_2bits("TCGT") # returns integer64 encoding
packed
#> integer64
#> [1] 231

# Can be vectorized for multiple sequences
packed_seqs <- pack_2bits(rep("TCGTGTCGATCTATGCTGATGTCGTGAT", 1e4))
head(packed_seqs)
#> integer64
#> [1] 57314016814210791 57314016814210791 57314016814210791 57314016814210791
#> [5] 57314016814210791 57314016814210791

# Unpack sequence
unpack_2bits(packed, 4) # returns "TCGT"
#> [1] "TCGT"

# Can be vectorized for multiple sequences
unpacked_seqs <- unpack_2bits(packed_seqs, k = 28)
head(unpacked_seqs)
#> [1] "TCGTGTCGATCTATGCTGATGTCGTGAT" "TCGTGTCGATCTATGCTGATGTCGTGAT"
#> [3] "TCGTGTCGATCTATGCTGATGTCGTGAT" "TCGTGTCGATCTATGCTGATGTCGTGAT"
#> [5] "TCGTGTCGATCTATGCTGATGTCGTGAT" "TCGTGTCGATCTATGCTGATGTCGTGAT"