Module AminoAcidPropertyPrior
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Module AminoAcidPropertyPrior

source code

Dirichlet mixture priors for amino acid data.

Functions [hide private]
 
getAATable()
Returns the amino acid property table used to derive the paramters of the Dirichlet mixture prior
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constructPropertyPrior(base, psum)
Constructs a Dirichlet mixture prior for amino acid alphabet based on nine chemical properties.
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printPropertyTable()
Pretty print of the amino acid property table.
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readUCSCPrior(filename)
Reads files in the UCSC Dirichlet Mixture prior (DMP) format (http://www.soe.ucsc.edu/compbio/dirichlets/) and converts them into PyMix DirichletMixturePrior objects.
source code
Function Details [hide private]

constructPropertyPrior(base, psum)

source code 

Constructs a Dirichlet mixture prior for amino acid alphabet based on nine chemical properties.

Parameters:
  • base - value of alpha parameters when a property is not present
  • psum - sum of all entries in each alpha parameter vector when a property is present
Returns:
DirichletMixturePrior object

readUCSCPrior(filename)

source code 

Reads files in the UCSC Dirichlet Mixture prior (DMP) format (http://www.soe.ucsc.edu/compbio/dirichlets/) and converts them into PyMix DirichletMixturePrior objects.

Note that the alphabet in the UCSC priors does not contain the gap symbol. For the output DirichletMixturePrior the gap symbol is introduced with a parameter value of 0.01 in all components.

Parameters:
  • filename - file in UCSC DMP format
Returns:
DirichletMixturePrior object