Module sequence 

Sequence encoding and manipulation utilities.

This module provides functions for encoding DNA sequences into compact bitmap representations and performing sequence analysis operations.

Overview

DNA sequences are encoded using a 2-bit representation where:

• A (adenine): 00
• C (cytosine): 01
• G (guanine): 10
• T/U (thymine/uracil): 11

This encoding reduces memory usage by 75% compared to ASCII representation and enables fast bitwise operations for sequence analysis.

Modules

• encoded: Encoded sequence structures with forward and reverse-complement
• io: FASTA file reading and parsing
• processing: Sequence analysis functions (GC content, codon detection)

Examples

Encode a sequence

use orphos_core::sequence::encoded::EncodedSequence;

let sequence = b"ATGAAACGCATTAGCACCACCATT";
let encoded = EncodedSequence::without_masking(sequence);

println!("Length: {} bp", encoded.sequence_length);
println!("GC content: {:.2}%", encoded.gc_content * 100.0);

Test for specific nucleotides

use orphos_core::sequence::{is_a, is_gc};
use orphos_core::sequence::encoded::EncodedSequence;

let sequence = b"ATGC";
let encoded = EncodedSequence::without_masking(sequence);

assert!(is_a(&encoded.forward_sequence, 0)); // Position 0 is 'A'
assert!(is_gc(&encoded.forward_sequence, 3)); // Position 3 is 'C'

Re-exports

pub use io::*;

pub use processing::*;

Modules

encoded

io

processing

Functions

calculate_background_mer_frequencies

Calculate background k-mer frequencies for both strands

calculate_kmer_index

Calculate k-mer index from sequence position for frequency analysis

char_to_nuc

Converts nucleotide character to 2-bit encoding for bitmap storage.

create_reverse_complement_sequence

Generate the reverse complement of an encoded DNA sequence

encode_sequence

Encode a DNA sequence into compact 2-bit representation

encode_sequence_simd_wide

SIMD-accelerated encoding using the wide crate with u8x32

encode_sequence_simd_wide_packed

Optimized packed encoding version with u8x32 and batch bit operations

find_max_reading_frame

Determine which of three reading frames has the highest score

gc_content

Calculate the GC content of a sequence region

is_a

Test if nucleotide at given position is adenine (A)

is_atg

Test if codon at position is ATG (methionine start codon)

is_c

Test if nucleotide at given position is cytosine (C)

is_g

Test if nucleotide at given position is guanine (G)

is_gc

Test if nucleotide at given position is G or C (high GC content indicator)

is_gtg

Test if codon at position is GTG (valine start codon)

is_n

Test if position contains an unknown nucleotide (N)

is_start

Test if codon at given position is a valid start codon

is_stop

Test if codon at given position is a stop codon

is_t

Test if nucleotide at given position is thymine (T)

is_ttg

Test if codon at position is TTG (leucine start codon)

mer_text

Convert k-mer index back to nucleotide sequence representation

min_of_two_integers

Return the minimum of two integers (utility function)

reverse_strand_reading_frame

Convert a forward strand reading frame to its corresponding reverse strand frame