Package Bio :: Package SeqUtils :: Module CodonUsage :: Class CodonAdaptationIndex
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Class CodonAdaptationIndex

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object --+
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        CodonAdaptationIndex

A codon adaptaion index (CAI) implementation.

This class implements the codon adaptaion index (CAI) described by Sharp and Li (Nucleic Acids Res. 1987 Feb 11;15(3):1281-95).

methods:

set_cai_index(Index):

This method sets-up an index to be used when calculating CAI for a gene. Just pass a dictionary similar to the SharpEcoliIndex in CodonUsageIndices module.

generate_index(FastaFile):

This method takes a location of a FastaFile and generates an index. This index can later be used to calculate CAI of a gene.

cai_for_gene(DNAsequence):

This method uses the Index (either the one you set or the one you generated) and returns the CAI for the DNA sequence.

print_index(): This method prints out the index you used.

NOTE - This implementation does not currently cope with alternative genetic codes, only the synonymous codons in the standard table are considered.

Instance Methods [hide private]
 
__init__(self)
x.__init__(...) initializes x; see help(type(x)) for signature
source code
 
set_cai_index(self, Index) source code
 
generate_index(self, FastaFile)
Generate a codon usage index from a FASTA file of CDS sequences.
source code
 
cai_for_gene(self, DNAsequence)
Calculate the CAI (float) for the provided DNA sequence (string).
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_count_codons(self, FastaFile) source code
 
print_index(self)
This method prints out the index you used.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

source code 

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)

generate_index(self, FastaFile)

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Generate a codon usage index from a FASTA file of CDS sequences.

This method takes a location of a Fasta file containing CDS sequences (which must all have a whole number of codons) and generates a codon usage index. This index can later be used to calculate CAI of a gene.

cai_for_gene(self, DNAsequence)

source code 

Calculate the CAI (float) for the provided DNA sequence (string).

This method uses the Index (either the one you set or the one you generated) and returns the CAI for the DNA sequence.