Data.Fasta.ByteString.Lazy.Translation

Collects all functions pertaining to the translation of nucleotides to amino acids for Lazy ByteString.

Documentation

chunksOf :: Int64 -> ByteString -> [ByteString]

Lazy ByteString version of chunksOf

codon2aa :: Codon -> Either ByteString AA

Converts a codon to an amino acid Remember, if there is an N in that DNA sequence, then it is translated as an X, an unknown amino acid.

customCodon2aa :: [(Codon, Char)] -> Codon -> Either ByteString AA

Translate a codon using a custom table

translate :: Int64 -> FastaSequence -> Either ByteString FastaSequence

Translates a bytestring of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a bytestring with the error if the codon is invalid.

customTranslate :: [(Codon, AA)] -> Int64 -> FastaSequence -> Either ByteString FastaSequence

Translates a bytestring of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a bytestring with the error if the codon is invalid. Also has customized codon translations as well overriding the defaults.