Amino Acids
Set of amino acid symbols also covers IUPAC amino acid symbols plus a gap symbol:
| Symbol | Constant | Meaning |
|---|---|---|
'A' | AA_A | Alanine |
'R' | AA_R | Arginine |
'N' | AA_N | Asparagine |
'D' | AA_D | Aspartic acid (Aspartate) |
'C' | AA_C | Cysteine |
'Q' | AA_Q | Glutamine |
'E' | AA_E | Glutamic acid (Glutamate) |
'G' | AA_G | Glycine |
'H' | AA_H | Histidine |
'I' | AA_I | Isoleucine |
'L' | AA_L | Leucine |
'K' | AA_K | Lysine |
'M' | AA_M | Methionine |
'F' | AA_F | Phenylalanine |
'P' | AA_P | Proline |
'S' | AA_S | Serine |
'T' | AA_T | Threonine |
'W' | AA_W | Tryptophan |
'Y' | AA_Y | Tyrosine |
'V' | AA_V | Valine |
'O' | AA_O | Pyrrolysine |
'U' | AA_U | Selenocysteine |
'B' | AA_B | Aspartic acid or Asparagine |
'J' | AA_J | Leucine or Isoleucine |
'Z' | AA_Z | Glutamine or Glutamic acid |
'X' | AA_X | Any amino acid |
'*' | AA_Term | Termination codon |
'-' | AA_Gap | Gap (none of the above) |
http://www.insdc.org/documents/feature_table.html#7.4.3
Symbols are accessible as constants with AA_ prefix:
julia> AA_A
AA_A
julia> AA_Q
AA_Q
julia> AA_Term
AA_Term
julia> typeof(AA_A)
AminoAcid
Symbols can be constructed by converting regular characters:
julia> convert(AminoAcid, 'A')
AA_A
julia> convert(AminoAcid, 'P') === AA_P
true
julia> convert(AminoAcid, 'a') === convert(AminoAcid, 'A')
true
3-letter and 1-letter abbreviations can be parsed using parse in a case-insensitive way:
julia> parse(AminoAcid, "Pro") # 3-letter abbreviation
AA_P
julia> parse(AminoAcid, "P") # 1-letter abbreviation
AA_P
julia> parse(AminoAcid, "Pro") == parse(AminoAcid, "pRo")
true
julia> tryparse(AminoAcid, "Pro") # tryparse returns either an amino acid or nothing
AA_P
julia> tryparse(AminoAcid, "Pr")