@@ -15,9 +15,9 @@ from Bio.Data import IUPACData # From the IUPAC definition at: # http://www.chem.qmw.ac.uk/iupac/AminoAcid/A2021.html#AA21 -# If you use X for selenocysteines, then you'll need a new alphabet. +assert IUPACData.extended_protein_letters == IUPACData.extended_protein_letters.upper() class ExtendedIUPACProtein(Alphabet.ProteinAlphabet): - """Extended IUPAC protein single letter alphabet including X etc. + """Extended uppercase IUPAC protein single letter alphabet including X etc. In addition to the standard 20 single letter protein codes, this includes: @@ -27,13 +27,17 @@ class ExtendedIUPACProtein(Alphabet.ProteinAlphabet): J = "Xle"; Leucine (L) or Isoleucine (I), used in mass-spec (NMR) U = "Sec"; Selenocysteine O = "Pyl"; Pyrrolysine + + This alphabet is not intended to be used with X for Selenocysteine + (an ad-hoc standard prior to the IUPAC adoption of U instead). """ letters = IUPACData.extended_protein_letters extended_protein = ExtendedIUPACProtein() +assert IUPACData.protein_letters == IUPACData.protein_letters.upper() class IUPACProtein(ExtendedIUPACProtein): - """IUPAC protein single letter alphabet of the 20 standard amino acids.""" + """Uppercase IUPAC protein single letter alphabet of the 20 standard amino acids.""" letters = IUPACData.protein_letters protein = IUPACProtein() @@ -43,11 +47,13 @@ protein = IUPACProtein() # The next two are the IUPAC definitions, from: # http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html class IUPACAmbiguousDNA(Alphabet.DNAAlphabet): + """Uppercase IUPAC ambiguous DNA.""" letters = IUPACData.ambiguous_dna_letters ambiguous_dna = IUPACAmbiguousDNA() class IUPACUnambiguousDNA(IUPACAmbiguousDNA): + """Uppercase IUPAC unambiguous DNA (letters GATC only).""" letters = IUPACData.unambiguous_dna_letters unambiguous_dna = IUPACUnambiguousDNA() @@ -55,22 +61,29 @@ unambiguous_dna = IUPACUnambiguousDNA() # Also from the URL, but not part of the standard class ExtendedIUPACDNA(Alphabet.DNAAlphabet): + """Extended IUPAC DNA alphabet. + + In addition to the standard letter codes GATC, this includes: + + B = 5-bromouridine + D = 5,6-dihydrouridine + S = thiouridine + W = wyosine + """ letters = IUPACData.extended_dna_letters - # B == 5-bromouridine - # D == 5,6-dihydrouridine - # S == thiouridine - # W == wyosine extended_dna = ExtendedIUPACDNA() ##################### RNA class IUPACAmbiguousRNA(Alphabet.RNAAlphabet): + """Uppercase IUPAC ambiguous RNA.""" letters = IUPACData.ambiguous_rna_letters ambiguous_rna = IUPACAmbiguousRNA() class IUPACUnambiguousRNA(IUPACAmbiguousRNA): + """Uppercase IUPAC unambiguous RNA (letters GAUC only).""" letters = IUPACData.unambiguous_rna_letters unambiguous_rna = IUPACUnambiguousRNA() Bio/Alphabet/IUPAC.py 95241abf3f2f4d45884966b97f591d43d6198e13 peterc peterc http://github.com/etal/biopython/commit/7da8341aa25a22904c993df66d8aee3ffdddc984 7da8341aa25a22904c993df66d8aee3ffdddc984 2008-12-07T09:22:48-08:00 2008-12-07T09:22:48-08:00 Docstrings 8989d04d88194ee208edf83dcd53cb7287b62ab2 peterc peterc