Package Bio :: Package Blast :: Module Record :: Class MultipleAlignment
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Class MultipleAlignment

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object --+
         |
        MultipleAlignment

Holds information about a multiple alignment.

Members: alignment A list of tuples (name, start residue, sequence, end residue).

The start residue is 1-based. It may be blank, if that sequence is not aligned in the multiple alignment.

Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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to_generic(self, alphabet)
Retrieve generic alignment object for the given alignment.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

to_generic(self, alphabet)

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Retrieve generic alignment object for the given alignment.

Instead of the tuples, this returns a MultipleSeqAlignment object from Bio.Align, through which you can manipulate and query the object.

alphabet is the specified alphabet for the sequences in the code (for example IUPAC.IUPACProtein).

Thanks to James Casbon for the code.