website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/Encodings/IUPACEncoding.py

   1 # Set up the IUPAC alphabet properties
   2
   3
   4 from Bio.PropertyManager import default_manager
   5 from Bio import Alphabet
   6 from Bio.Alphabet import IUPAC
   7 from Bio.Data import IUPACData
   8
   9 from Bio import Transcribe, Translate
  10
  11 set_prop = default_manager.class_property
  12
  13 # weight tables
  14 set_prop[IUPAC.IUPACUnambiguousDNA]["weight_table"] = \
  15              IUPACData.unambiguous_dna_weights
  16 set_prop[IUPAC.IUPACAmbiguousDNA]["weight_table"] = \
  17              IUPACData.avg_ambiguous_dna_weights
  18 set_prop[IUPAC.IUPACUnambiguousRNA]["weight_table"] = \
  19              IUPACData.unambiguous_rna_weights
  20 set_prop[IUPAC.IUPACAmbiguousRNA]["weight_table"] = \
  21              IUPACData.avg_ambiguous_rna_weights
  22 set_prop[IUPAC.IUPACProtein]["weight_table"] = \
  23              IUPACData.protein_weights
  24 set_prop[IUPAC.ExtendedIUPACProtein]["weight_table"] = \
  25              IUPACData.avg_extended_protein_weights
  26
  27 set_prop[IUPAC.IUPACUnambiguousDNA]["weight_range_table"] = \
  28              IUPACData.unambiguous_dna_weight_ranges
  29 set_prop[IUPAC.IUPACAmbiguousDNA]["weight_range_table"] = \
  30              IUPACData.ambiguous_dna_weight_ranges
  31 set_prop[IUPAC.IUPACUnambiguousRNA]["weight_range_table"] = \
  32              IUPACData.unambiguous_rna_weight_ranges
  33 set_prop[IUPAC.IUPACAmbiguousRNA]["weight_range_table"] = \
  34              IUPACData.ambiguous_rna_weight_ranges
  35 set_prop[IUPAC.IUPACProtein]["weight_range_table"] = \
  36              IUPACData.protein_weight_ranges
  37 set_prop[IUPAC.ExtendedIUPACProtein]["weight_range_table"] = \
  38              IUPACData.extended_protein_weight_ranges
  39
  40
  41
  42 #  transcriber objects
  43
  44 set_prop[Alphabet.DNAAlphabet]["transcriber"] = \
  45              Transcribe.generic_transcriber
  46
  47 set_prop[IUPAC.IUPACAmbiguousDNA]["transcriber"] = \
  48              Transcribe.ambiguous_transcriber
  49
  50 set_prop[IUPAC.IUPACUnambiguousDNA]["transcriber"] = \
  51              Transcribe.unambiguous_transcriber
  52
  53
  54 set_prop[Alphabet.RNAAlphabet]["transcriber"] = \
  55              Transcribe.generic_transcriber
  56
  57 set_prop[IUPAC.IUPACAmbiguousRNA]["transcriber"] = \
  58              Transcribe.ambiguous_transcriber
  59
  60 set_prop[IUPAC.IUPACUnambiguousRNA]["transcriber"] = \
  61              Transcribe.unambiguous_transcriber
  62
  63
  64 # translator objects
  65 for name, obj in Translate.unambiguous_dna_by_name.items():
  66     property = "translator.name." + name
  67     set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
  68     set_prop[obj.table.protein_alphabet.__class__][property] = obj
  69
  70 for name, obj in Translate.unambiguous_rna_by_name.items():
  71     property = "translator.name." + name
  72     set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
  73     property = "rna_translator.name." + name
  74     set_prop[obj.table.protein_alphabet.__class__][property] = obj
  75
  76
  77 for id, obj in Translate.unambiguous_dna_by_id.items():
  78     property = "translator.id.%d" % id
  79     set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
  80     set_prop[obj.table.protein_alphabet.__class__][property] = obj
  81     if id == 1:
  82         set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
  83         set_prop[obj.table.protein_alphabet.__class__]["translator"] = obj
  84
  85
  86 for id, obj in Translate.unambiguous_rna_by_id.items():
  87     property = "translator.id.%d" % id
  88     set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
  89     property = "rna_translator.id.%d" % id
  90     set_prop[obj.table.protein_alphabet.__class__][property] = obj
  91     if id == 1:
  92         set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
  93         set_prop[obj.table.protein_alphabet.__class__]["rna_translator"] = obj
  94
  95 # ambiguous translator objects
  96 for name, obj in Translate.ambiguous_dna_by_name.items():
  97     property = "translator.name." + name
  98     set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
  99     property = "ambiguous_translator.name." + name
 100     set_prop[obj.table.protein_alphabet.__class__][property] = obj
 101
 102 for name, obj in Translate.ambiguous_rna_by_name.items():
 103     property = "translator.name." + name
 104     set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
 105     property = "ambiguous_rna_translator.name." + name
 106     set_prop[obj.table.protein_alphabet.__class__][property] = obj
 107
 108
 109 for id, obj in Translate.ambiguous_dna_by_id.items():
 110     property = "translator.id.%d" % id
 111     set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
 112     property = "ambiguous_translator.id.%d" % id
 113     set_prop[obj.table.protein_alphabet.__class__][property] = obj
 114     if id == 1:
 115         set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
 116         set_prop[obj.table.protein_alphabet.__class__]["ambiguous_translator"] = obj
 117
 118
 119 for id, obj in Translate.ambiguous_rna_by_id.items():
 120     property = "translator.id.%d" % id
 121     set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
 122     property = "ambiguous_rna_translator.id.%d" % id
 123     set_prop[obj.table.protein_alphabet.__class__][property] = obj
 124     if id == 1:
 125         set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
 126         set_prop[obj.table.protein_alphabet.__class__]["ambiguous_rna_translator"] = obj