1 """Properties once used for transcription and translation (DEPRECATED).
2
3 This module is deprecated, and is expected to be removed in the next release.
4 If you use this module, please contact the Biopython developers via the
5 mailing lists.
6 """
7
8
9
10
11
12 from Bio.PropertyManager import default_manager
13 from Bio import Alphabet
14 from Bio.Alphabet import IUPAC
15 from Bio.Data import IUPACData
16
17 from Bio import Transcribe, Translate
18
19 set_prop = default_manager.class_property
20
21
22 set_prop[IUPAC.IUPACUnambiguousDNA]["weight_table"] = \
23 IUPACData.unambiguous_dna_weights
24 set_prop[IUPAC.IUPACAmbiguousDNA]["weight_table"] = \
25 IUPACData.avg_ambiguous_dna_weights
26 set_prop[IUPAC.IUPACUnambiguousRNA]["weight_table"] = \
27 IUPACData.unambiguous_rna_weights
28 set_prop[IUPAC.IUPACAmbiguousRNA]["weight_table"] = \
29 IUPACData.avg_ambiguous_rna_weights
30 set_prop[IUPAC.IUPACProtein]["weight_table"] = \
31 IUPACData.protein_weights
32 set_prop[IUPAC.ExtendedIUPACProtein]["weight_table"] = \
33 IUPACData.avg_extended_protein_weights
34
35 set_prop[IUPAC.IUPACUnambiguousDNA]["weight_range_table"] = \
36 IUPACData.unambiguous_dna_weight_ranges
37 set_prop[IUPAC.IUPACAmbiguousDNA]["weight_range_table"] = \
38 IUPACData.ambiguous_dna_weight_ranges
39 set_prop[IUPAC.IUPACUnambiguousRNA]["weight_range_table"] = \
40 IUPACData.unambiguous_rna_weight_ranges
41 set_prop[IUPAC.IUPACAmbiguousRNA]["weight_range_table"] = \
42 IUPACData.ambiguous_rna_weight_ranges
43 set_prop[IUPAC.IUPACProtein]["weight_range_table"] = \
44 IUPACData.protein_weight_ranges
45 set_prop[IUPAC.ExtendedIUPACProtein]["weight_range_table"] = \
46 IUPACData.extended_protein_weight_ranges
47
48
49
50
51
52 set_prop[Alphabet.DNAAlphabet]["transcriber"] = \
53 Transcribe.generic_transcriber
54
55 set_prop[IUPAC.IUPACAmbiguousDNA]["transcriber"] = \
56 Transcribe.ambiguous_transcriber
57
58 set_prop[IUPAC.IUPACUnambiguousDNA]["transcriber"] = \
59 Transcribe.unambiguous_transcriber
60
61
62 set_prop[Alphabet.RNAAlphabet]["transcriber"] = \
63 Transcribe.generic_transcriber
64
65 set_prop[IUPAC.IUPACAmbiguousRNA]["transcriber"] = \
66 Transcribe.ambiguous_transcriber
67
68 set_prop[IUPAC.IUPACUnambiguousRNA]["transcriber"] = \
69 Transcribe.unambiguous_transcriber
70
71
72
73 for name, obj in Translate.unambiguous_dna_by_name.iteritems():
74 property = "translator.name." + name
75 set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
76 set_prop[obj.table.protein_alphabet.__class__][property] = obj
77
78 for name, obj in Translate.unambiguous_rna_by_name.iteritems():
79 property = "translator.name." + name
80 set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
81 property = "rna_translator.name." + name
82 set_prop[obj.table.protein_alphabet.__class__][property] = obj
83
84
85 for id, obj in Translate.unambiguous_dna_by_id.iteritems():
86 property = "translator.id.%d" % id
87 set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
88 set_prop[obj.table.protein_alphabet.__class__][property] = obj
89 if id == 1:
90 set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
91 set_prop[obj.table.protein_alphabet.__class__]["translator"] = obj
92
93
94 for id, obj in Translate.unambiguous_rna_by_id.iteritems():
95 property = "translator.id.%d" % id
96 set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
97 property = "rna_translator.id.%d" % id
98 set_prop[obj.table.protein_alphabet.__class__][property] = obj
99 if id == 1:
100 set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
101 set_prop[obj.table.protein_alphabet.__class__]["rna_translator"] = obj
102
103
104 for name, obj in Translate.ambiguous_dna_by_name.iteritems():
105 property = "translator.name." + name
106 set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
107 property = "ambiguous_translator.name." + name
108 set_prop[obj.table.protein_alphabet.__class__][property] = obj
109
110 for name, obj in Translate.ambiguous_rna_by_name.iteritems():
111 property = "translator.name." + name
112 set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
113 property = "ambiguous_rna_translator.name." + name
114 set_prop[obj.table.protein_alphabet.__class__][property] = obj
115
116
117 for id, obj in Translate.ambiguous_dna_by_id.iteritems():
118 property = "translator.id.%d" % id
119 set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
120 property = "ambiguous_translator.id.%d" % id
121 set_prop[obj.table.protein_alphabet.__class__][property] = obj
122 if id == 1:
123 set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
124 set_prop[obj.table.protein_alphabet.__class__]["ambiguous_translator"] = obj
125
126
127 for id, obj in Translate.ambiguous_rna_by_id.iteritems():
128 property = "translator.id.%d" % id
129 set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
130 property = "ambiguous_rna_translator.id.%d" % id
131 set_prop[obj.table.protein_alphabet.__class__][property] = obj
132 if id == 1:
133 set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
134 set_prop[obj.table.protein_alphabet.__class__]["ambiguous_rna_translator"] = obj
135