Package Bio :: Package AlignIO :: Module NexusIO
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Module NexusIO

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Bio.AlignIO support for the "nexus" file format.

You are expected to use this module via the Bio.AlignIO functions (or the Bio.SeqIO functions if you want to work directly with the gapped sequences).

See also the Bio.Nexus module (which this code calls internally), as this offers more than just accessing the alignment or its sequences as SeqRecord objects.

Classes [hide private]
Nexus alignment writer.
Functions [hide private]
NexusIterator(handle, seq_count=None)
Return SeqRecord objects from a Nexus file.
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Variables [hide private]
  __package__ = 'Bio.AlignIO'
Function Details [hide private]

NexusIterator(handle, seq_count=None)

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Return SeqRecord objects from a Nexus file.

Thus uses the Bio.Nexus module to do the hard work.

You are expected to call this function via Bio.SeqIO or Bio.AlignIO (and not use it directly).

NOTE - We only expect ONE alignment matrix per Nexus file, meaning this iterator will only yield one MultipleSeqAlignment.