Package Bio :: Package Align :: Module AlignInfo :: Class PSSM
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Class PSSM

source code

object --+
         |
        PSSM

Represent a position specific score matrix.

This class is meant to make it easy to access the info within a PSSM
and also make it easy to print out the information in a nice table.

Let's say you had an alignment like this:
GTATC
AT--C
CTGTC

The position specific score matrix (when printed) looks like:

  G A T C
G 1 1 0 1
T 0 0 3 0
A 1 1 0 0
T 0 0 2 0
C 0 0 0 3

You can access a single element of the PSSM using the following:

your_pssm[sequence_number][residue_count_name]

For instance, to get the 'T' residue for the second element in the
above alignment you would need to do:

your_pssm[1]['T']

Instance Methods [hide private]
 
__init__(self, pssm)
Initialize with pssm data to represent.
source code
 
__getitem__(self, pos) source code
 
__str__(self)
str(x)
source code
 
get_residue(self, pos)
Return the residue letter at the specified position.
source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, pssm)
(Constructor)

source code 
Initialize with pssm data to represent.

The pssm passed should be a list with the following structure:

list[0] - The letter of the residue being represented (for instance,
from the example above, the first few list[0]s would be GTAT...
list[1] - A dictionary with the letter substitutions and counts.

Overrides: object.__init__

__str__(self)
(Informal representation operator)

source code 
str(x)

Overrides: object.__str__
(inherited documentation)