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use debruijn::dna_string::DnaString;
use debruijn::Mer;
use string_utils::strme;
pub fn have_start(b: &DnaString, j: usize) -> bool {
let (a, g, t) = (0u8, 2u8, 3u8);
if b.get(j) == a && b.get(j + 1) == t && b.get(j + 2) == g {
return true;
}
false
}
pub fn have_stop(b: &DnaString, j: usize) -> bool {
let (a, g, t) = (0u8, 2u8, 3u8);
if b.get(j) == t && b.get(j + 1) == a && b.get(j + 2) == g {
return true;
}
if b.get(j) == t && b.get(j + 1) == a && b.get(j + 2) == a {
return true;
}
if b.get(j) == t && b.get(j + 1) == g && b.get(j + 2) == a {
return true;
}
false
}
pub fn aa3_to_aa(aa3: &[u8]) -> u8 {
assert!(aa3.len() == 3);
let aa = match aa3 {
b"ALA" => b'A',
b"ARG" => b'R',
b"ASN" => b'N',
b"ASP" => b'D',
b"CYS" => b'C',
b"GLU" => b'E',
b"GLN" => b'Q',
b"GLY" => b'G',
b"HIS" => b'H',
b"ILE" => b'I',
b"LYS" => b'K',
b"LEU" => b'L',
b"MET" => b'M',
b"PHE" => b'F',
b"PRO" => b'P',
b"SER" => b'S',
b"THR" => b'T',
b"TRP" => b'W',
b"TYR" => b'Y',
b"VAL" => b'V',
_ => panic!("Unexpected three-letter amino acid code {}.", strme(aa3)),
};
aa
}
pub fn codon_to_aa(codon: &[u8]) -> u8 {
assert!(codon.len() == 3);
let aa = match codon {
b"GGT" => b'G',
b"GGC" => b'G',
b"GGA" => b'G',
b"GGG" => b'G',
b"TGG" => b'W',
b"TGT" => b'C',
b"TGC" => b'C',
b"TTT" => b'F',
b"TTC" => b'F',
b"TTA" => b'L',
b"TTG" => b'L',
b"CTT" => b'L',
b"CTC" => b'L',
b"CTA" => b'L',
b"CTG" => b'L',
b"ATT" => b'I',
b"ATC" => b'I',
b"ATA" => b'I',
b"GTT" => b'V',
b"GTC" => b'V',
b"GTA" => b'V',
b"GTG" => b'V',
b"TCT" => b'S',
b"TCC" => b'S',
b"TCA" => b'S',
b"TCG" => b'S',
b"AGT" => b'S',
b"AGC" => b'S',
b"CCT" => b'P',
b"CCC" => b'P',
b"CCA" => b'P',
b"CCG" => b'P',
b"ACT" => b'T',
b"ACC" => b'T',
b"ACA" => b'T',
b"ACG" => b'T',
b"GCT" => b'A',
b"GCC" => b'A',
b"GCA" => b'A',
b"GCG" => b'A',
b"TAT" => b'Y',
b"TAC" => b'Y',
b"CAT" => b'H',
b"CAC" => b'H',
b"CAA" => b'Q',
b"CAG" => b'Q',
b"AAT" => b'N',
b"AAC" => b'N',
b"AAA" => b'K',
b"AAG" => b'K',
b"GAT" => b'D',
b"GAC" => b'D',
b"GAA" => b'E',
b"GAG" => b'E',
b"CGT" => b'R',
b"CGC" => b'R',
b"CGA" => b'R',
b"CGG" => b'R',
b"AGA" => b'R',
b"AGG" => b'R',
b"ATG" => b'M',
b"TAG" => b'*',
b"TAA" => b'*',
b"TGA" => b'*',
_ => panic!("Unexpected codon {}.", strme(codon)),
};
aa
}
pub fn aa_seq(x: &[u8], start: usize) -> Vec<u8> {
let mut a = Vec::<u8>::new();
if x.len() >= 3 {
for j in (start..x.len() - 3 + 1).step_by(3) {
if x[j] == b'-' && x[j + 1] == b'-' && x[j + 2] == b'-' {
a.push(b'-');
} else {
a.push(codon_to_aa(&x[j..j + 3]));
}
}
}
a
}
