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Package Bio :: Package Align :: Module AlignInfo :: Class PSSM |
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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']
Method Summary | |
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Initialize with pssm data to represent. | |
__getitem__(self,
pos)
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__str__(self)
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Return the residue letter at the specified position. |
Method Details |
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__init__(self,
pssm)
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get_residue(self, pos)Return the residue letter at the specified position. |
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