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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']
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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. |
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