Class: PSSM

Class: PSSM Bio/Align/AlignInfo.py

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

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']

Methods
Methods	__getitem__ __init__ __str__ get_residue
	__getitem__
	__getitem__ ( self, pos )
	__init__
	__init__ ( self, pssm ) 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.
	__str__
	__str__ ( self )
	get_residue
	get_residue ( self, pos ) Return the residue letter at the specified position.

This document was automatically generated on Mon Jul 1 12:02:43 2002 by HappyDoc version 2.0.1