Package Bio :: Package AlignIO :: Module NexusIO :: Class NexusWriter

Class NexusWriter

Interfaces.AlignmentWriter --+
                             |
                            NexusWriter

Nexus alignment writer.

Note that Nexus files are only expected to hold ONE alignment matrix.

You are expected to call this class via the Bio.AlignIO.write() or Bio.SeqIO.write() functions.

Instance Methods

[hide private]

write_file(self, alignments)
Use this to write an entire file containing the given alignments.

source code

write_alignment(self, alignment)

source code

_classify_alphabet_for_nexus(self, alphabet)
Returns 'protein', 'dna', 'rna' based on the alphabet (PRIVATE).

source code

Inherited from Interfaces.AlignmentWriter: __init__, clean

Method Details

[hide private]

write_file(self, alignments)

source code

Use this to write an entire file containing the given alignments.

alignments - A list or iterator returning MultipleSeqAlignment objects.
             This should hold ONE and only one alignment.

Overrides: Interfaces.AlignmentWriter.write_file

_classify_alphabet_for_nexus(self, alphabet)

source code

Returns 'protein', 'dna', 'rna' based on the alphabet (PRIVATE).

Raises an exception if this is not possible.