| Safe Haskell | Safe |
|---|---|
| Language | Haskell98 |
Data.Fasta.Text.Translation
Description
Collects all functions pertaining to the translation of nucleotides to amino acids for Text.
- codon2aa :: Codon -> Either Text AA
- customCodon2aa :: [(Codon, Char)] -> Codon -> Either Text AA
- translate :: Int -> FastaSequence -> Either Text FastaSequence
- customTranslate :: [(Codon, AA)] -> Int -> FastaSequence -> Either Text FastaSequence
Documentation
codon2aa :: Codon -> Either Text AA Source #
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 Text AA Source #
Translate a codon using a custom table
translate :: Int -> FastaSequence -> Either Text FastaSequence Source #
Translates a text of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a text with the error if the codon is invalid.
customTranslate :: [(Codon, AA)] -> Int -> FastaSequence -> Either Text FastaSequence Source #
Translates a text of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a text with the error if the codon is invalid. Also has customized codon translations as well overriding the defaults.