Adding deepcopy patch back in. See bug #2380.

biopython · Jun 29, 2008 · 22853c1 · 22853c1
1 parent 56eb84b
commit 22853c1
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/Bio/Nexus/Nexus.py b/Bio/Nexus/Nexus.py
@@ -666,17 +666,17 @@ def _format(self,options):
         if options.has_key('datatype'):
             self.datatype=options['datatype'].lower()
             if self.datatype=='dna' or self.datatype=='nucleotide':
-                self.alphabet=IUPAC.ambiguous_dna
-                self.ambiguous_values=IUPACData.ambiguous_dna_values
-                self.unambiguous_letters=IUPACData.unambiguous_dna_letters
+                self.alphabet=copy.deepcopy(IUPAC.ambiguous_dna)
+                self.ambiguous_values=copy.deepcopy(IUPACData.ambiguous_dna_values)
+                self.unambiguous_letters=copy.deepcopy(IUPACData.unambiguous_dna_letters)
             elif self.datatype=='rna':
-                self.alphabet=IUPAC.ambiguous_rna
-                self.ambiguous_values=IUPACData.ambiguous_rna_values
-                self.unambiguous_letters=IUPACData.unambiguous_rna_letters
+                self.alphabet=copy.deepcopy(IUPAC.ambiguous_rna)
+                self.ambiguous_values=copy.deepcopy(IUPACData.ambiguous_rna_values)
+                self.unambiguous_letters=copy.deepcopy(IUPACData.unambiguous_rna_letters)
             elif self.datatype=='protein':
-                self.alphabet=IUPAC.protein
-                self.ambiguous_values={'B':'DN','Z':'EQ','X':IUPACData.protein_letters} # that's how PAUP handles it
-                self.unambiguous_letters=IUPACData.protein_letters+'*' # stop-codon
+                self.alphabet=copy.deepcopy(IUPAC.protein)
+                self.ambiguous_values={'B':'DN','Z':'EQ','X':copy.deepcopy(IUPACData.protein_letters)} # that's how PAUP handles it
+                self.unambiguous_letters=copy.deepcopy(IUPACData.protein_letters)+'*' # stop-codon
             elif self.datatype=='standard':
                 raise NexusError('Datatype standard is not yet supported.')
                 #self.alphabet=None