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8 """Standard nucleotide and protein alphabets defined by IUPAC."""
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10 from Bio import Alphabet
11 from Bio.Data import IUPACData
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18 assert IUPACData.extended_protein_letters == IUPACData.extended_protein_letters.upper()
20 """Extended uppercase IUPAC protein single letter alphabet including X etc.
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22 In addition to the standard 20 single letter protein codes, this includes:
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24 B = "Asx"; Aspartic acid (R) or Asparagine (N)
25 X = "Xxx"; Unknown or 'other' amino acid
26 Z = "Glx"; Glutamic acid (E) or Glutamine (Q)
27 J = "Xle"; Leucine (L) or Isoleucine (I), used in mass-spec (NMR)
28 U = "Sec"; Selenocysteine
29 O = "Pyl"; Pyrrolysine
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31 This alphabet is not intended to be used with X for Selenocysteine
32 (an ad-hoc standard prior to the IUPAC adoption of U instead).
33 """
34 letters = IUPACData.extended_protein_letters
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36 extended_protein = ExtendedIUPACProtein()
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38 assert IUPACData.protein_letters == IUPACData.protein_letters.upper()
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43 protein = IUPACProtein()
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53 ambiguous_dna = IUPACAmbiguousDNA()
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59 unambiguous_dna = IUPACUnambiguousDNA()
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64 """Extended IUPAC DNA alphabet.
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66 In addition to the standard letter codes GATC, this includes:
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68 B = 5-bromouridine
69 D = 5,6-dihydrouridine
70 S = thiouridine
71 W = wyosine
72 """
73 letters = IUPACData.extended_dna_letters
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75 extended_dna = ExtendedIUPACDNA()
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83 ambiguous_rna = IUPACAmbiguousRNA()
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89 unambiguous_rna = IUPACUnambiguousRNA()
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105 from Bio.PropertyManager import default_manager
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121 default_manager.class_resolver[IUPACProtein] = _bootstrap
122 default_manager.class_resolver[ExtendedIUPACProtein] = _bootstrap
123 default_manager.class_resolver[IUPACAmbiguousDNA] = _bootstrap
124 default_manager.class_resolver[IUPACUnambiguousDNA] = _bootstrap
125 default_manager.class_resolver[ExtendedIUPACDNA] = _bootstrap
126 default_manager.class_resolver[IUPACAmbiguousRNA] = _bootstrap
127 default_manager.class_resolver[IUPACUnambiguousRNA] = _bootstrap
128