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src/b/i/biopython-1.63/Bio/AlignIO/NexusIO.py   biopython(Download)
        #in the output - something MrBayes can't handle.
        #TODO - Default to always interleaving?
        n.write_nexus_data(self.handle, interleave=(columns > 1000))
 
    def _classify_alphabet_for_nexus(self, alphabet):

src/b/i/biopython-HEAD/Bio/AlignIO/NexusIO.py   biopython(Download)
        #in the output - something MrBayes can't handle.
        #TODO - Default to always interleaving?
        n.write_nexus_data(self.handle, interleave=(columns > 1000))
 
    def _classify_alphabet_for_nexus(self, alphabet):

src/b/i/biopython-1.63/Tests/test_Nexus.py   biopython(Download)
            os.remove(filename)
        n = Nexus.Nexus(self.handle)
        n.write_nexus_data(filename)
        self.assertTrue(os.path.isfile(filename))
        os.remove(filename)
        # and exporting adjusted sets
        f1=tempfile.NamedTemporaryFile("w+")
        n.write_nexus_data(f1,
                           delete=['t1', 't7'],
                           exclude=n.invert(n.charsets['big']))
 
        f2=tempfile.NamedTemporaryFile("w+")
        n.write_nexus_data(f2,
                           delete=['t2_the_name'],
                           exclude=list(range(3, 40, 4)))

src/b/i/biopython-HEAD/Tests/test_Nexus.py   biopython(Download)
            os.remove(filename)
        n = Nexus.Nexus(self.handle)
        n.write_nexus_data(filename)
        self.assertTrue(os.path.isfile(filename))
        os.remove(filename)
        # and exporting adjusted sets
        f1=tempfile.NamedTemporaryFile("w+")
        n.write_nexus_data(f1,
                           delete=['t1', 't7'],
                           exclude=n.invert(n.charsets['big']))
 
        f2=tempfile.NamedTemporaryFile("w+")
        n.write_nexus_data(f2,
                           delete=['t2_the_name'],
                           exclude=list(range(3, 40, 4)))