Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / Encodings / IUPACEncoding.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Encodings/IUPACEncoding.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Encodings/IUPACEncoding.py
new file mode 100644 (file)
index 0000000..a4089a3
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+++ b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Encodings/IUPACEncoding.py
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+# Set up the IUPAC alphabet properties
+
+
+from Bio.PropertyManager import default_manager
+from Bio import Alphabet
+from Bio.Alphabet import IUPAC
+from Bio.Data import IUPACData
+
+from Bio import Transcribe, Translate
+
+set_prop = default_manager.class_property
+
+# weight tables
+set_prop[IUPAC.IUPACUnambiguousDNA]["weight_table"] = \
+             IUPACData.unambiguous_dna_weights
+set_prop[IUPAC.IUPACAmbiguousDNA]["weight_table"] = \
+             IUPACData.avg_ambiguous_dna_weights
+set_prop[IUPAC.IUPACUnambiguousRNA]["weight_table"] = \
+             IUPACData.unambiguous_rna_weights
+set_prop[IUPAC.IUPACAmbiguousRNA]["weight_table"] = \
+             IUPACData.avg_ambiguous_rna_weights
+set_prop[IUPAC.IUPACProtein]["weight_table"] = \
+             IUPACData.protein_weights
+set_prop[IUPAC.ExtendedIUPACProtein]["weight_table"] = \
+             IUPACData.avg_extended_protein_weights
+
+set_prop[IUPAC.IUPACUnambiguousDNA]["weight_range_table"] = \
+             IUPACData.unambiguous_dna_weight_ranges
+set_prop[IUPAC.IUPACAmbiguousDNA]["weight_range_table"] = \
+             IUPACData.ambiguous_dna_weight_ranges
+set_prop[IUPAC.IUPACUnambiguousRNA]["weight_range_table"] = \
+             IUPACData.unambiguous_rna_weight_ranges
+set_prop[IUPAC.IUPACAmbiguousRNA]["weight_range_table"] = \
+             IUPACData.ambiguous_rna_weight_ranges
+set_prop[IUPAC.IUPACProtein]["weight_range_table"] = \
+             IUPACData.protein_weight_ranges
+set_prop[IUPAC.ExtendedIUPACProtein]["weight_range_table"] = \
+             IUPACData.extended_protein_weight_ranges
+
+
+
+#  transcriber objects
+
+set_prop[Alphabet.DNAAlphabet]["transcriber"] = \
+             Transcribe.generic_transcriber
+
+set_prop[IUPAC.IUPACAmbiguousDNA]["transcriber"] = \
+             Transcribe.ambiguous_transcriber
+
+set_prop[IUPAC.IUPACUnambiguousDNA]["transcriber"] = \
+             Transcribe.unambiguous_transcriber
+
+
+set_prop[Alphabet.RNAAlphabet]["transcriber"] = \
+             Transcribe.generic_transcriber
+
+set_prop[IUPAC.IUPACAmbiguousRNA]["transcriber"] = \
+             Transcribe.ambiguous_transcriber
+
+set_prop[IUPAC.IUPACUnambiguousRNA]["transcriber"] = \
+             Transcribe.unambiguous_transcriber
+
+
+# translator objects
+for name, obj in Translate.unambiguous_dna_by_name.items():
+    property = "translator.name." + name
+    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+    set_prop[obj.table.protein_alphabet.__class__][property] = obj
+
+for name, obj in Translate.unambiguous_rna_by_name.items():
+    property = "translator.name." + name
+    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+    property = "rna_translator.name." + name
+    set_prop[obj.table.protein_alphabet.__class__][property] = obj
+
+
+for id, obj in Translate.unambiguous_dna_by_id.items():
+    property = "translator.id.%d" % id
+    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+    set_prop[obj.table.protein_alphabet.__class__][property] = obj
+    if id == 1:
+        set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
+        set_prop[obj.table.protein_alphabet.__class__]["translator"] = obj
+
+
+for id, obj in Translate.unambiguous_rna_by_id.items():
+    property = "translator.id.%d" % id
+    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+    property = "rna_translator.id.%d" % id
+    set_prop[obj.table.protein_alphabet.__class__][property] = obj
+    if id == 1:
+        set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
+        set_prop[obj.table.protein_alphabet.__class__]["rna_translator"] = obj
+
+# ambiguous translator objects
+for name, obj in Translate.ambiguous_dna_by_name.items():
+    property = "translator.name." + name
+    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+    property = "ambiguous_translator.name." + name
+    set_prop[obj.table.protein_alphabet.__class__][property] = obj
+
+for name, obj in Translate.ambiguous_rna_by_name.items():
+    property = "translator.name." + name
+    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+    property = "ambiguous_rna_translator.name." + name
+    set_prop[obj.table.protein_alphabet.__class__][property] = obj
+
+
+for id, obj in Translate.ambiguous_dna_by_id.items():
+    property = "translator.id.%d" % id
+    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+    property = "ambiguous_translator.id.%d" % id
+    set_prop[obj.table.protein_alphabet.__class__][property] = obj
+    if id == 1:
+        set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
+        set_prop[obj.table.protein_alphabet.__class__]["ambiguous_translator"] = obj
+
+
+for id, obj in Translate.ambiguous_rna_by_id.items():
+    property = "translator.id.%d" % id
+    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
+    property = "ambiguous_rna_translator.id.%d" % id
+    set_prop[obj.table.protein_alphabet.__class__][property] = obj
+    if id == 1:
+        set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
+        set_prop[obj.table.protein_alphabet.__class__]["ambiguous_rna_translator"] = obj