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 adaptation index (CAI) implementation.

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

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
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set_cai_index(self, index)
Sets up an index to be used when calculating CAI for a gene.
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generate_index(self, fasta_file)
Generate a codon usage index from a FASTA file of CDS sequences.
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cai_for_gene(self, dna_sequence)
Calculate the CAI (float) for the provided DNA sequence (string).
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_count_codons(self, fasta_file) source code
 
print_index(self)
Prints out the index 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)

set_cai_index(self, index)

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

generate_index(self, fasta_file)

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

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.

cai_for_gene(self, dna_sequence)

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.