ó LIc@sbddlZddlmZddlmZi@dd6dd6dd6dd6dd 6dd 6dd 6dd 6dd 6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd 6dd!6dd"6dd#6dd$6dd%6dd&6dd'6dd(6dd)6dd*6dd+6dd,6dd-6dd.6dd/6dd06dd16dd26dd36dd46dd56dd66dd76dd86dd96dd:6dd;6dd<6dd=6dd>6dd?6dd@6ddA6ddB6ddC6ddD6Zid5d6gdE6d!d"gdF6d%d(d'd&d>d=gdG6ddgdH6dgdI6ddgdJ6d)d,d+d*gdK6d dgdL6dd7dgdM6d.d/d0d-gdN6ddgdO6d3d2d4d1gdP6dAdDdCdBgdQ6ddd gdR6ddd d d d gdS6ddgdT6d;d:d<d9d@d?gdU6d8gdV6ddddgdW6d$d#gdX6ddgdY6ZdZd\d[„ƒYZdS(]iÿÿÿÿN(tSharpEcoliIndex(tSeqIOitTTTtTTCtTTAtTTGtCTTtCTCtCTAtCTGtATTtATCtATAtATGtGTTtGTCtGTAtGTGtTATtTACtTAAtTAGtCATtCACtCAAtCAGtAATtAACtAAAtAAGtGATtGACtGAAtGAGtTCTtTCCtTCAtTCGtCCTtCCCtCCAtCCGtACTtACCtACAtACGtGCTtGCCtGCAtGCGtTGTtTGCtTGAtTGGtCGTtCGCtCGAtCGGtAGTtAGCtAGAtAGGtGGTtGGCtGGAtGGGtCYStASPtSERtGLNtMETtASNtPROtLYStSTOPtTHRtPHEtALAtGLYtILEtLEUtHIStARGtTRPtVALtGLUtTYRtCodonAdaptationIndexcBsDeZdZd„Zd„Zd„Zd„Zd„Zd„ZRS(s·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. cCsi|_i|_dS(N(tindext codon_count(tself((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqUtils/CodonUsage.pyt__init__?s cCs ||_dS(N(RX(RZtIndex((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SeqUtils/CodonUsage.pyt set_cai_indexDscCs|jiks|jikr-tdƒ‚n|j|ƒxÏtjƒD]Á}d}g}x#t|D]}||j|7}qdWx<t|D]0}|j|j|dtt|ƒ|ƒqŠWt|ƒ}x;t tt|ƒƒD]#}||||jt||s4 &###########$ # #&#0