B bA@sldZddlZddlmZddlmZddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddd@Zddgd d gd d d dddgddgdgddgddddgddgdddgdd d!d"gd#d$gd%d&d'd(gd)d*d+d,gd-d.d/gd0d1d2d3d4d5gd6d7gd8d9d:d;dgd?d@dAdBgdCdDgdEdFgdGZGdHdIdIZdS)Jz%Methods for codon usage calculations.N)SharpEcoliIndex)SeqIO)@TTTTTCTTATTGCTTCTCCTACTGATTATCATAATGGTTGTCGTAGTGTATTACTAATAGCATCACCAACAGAATAACAAAAAGGATGACGAAGAGTCTTCCTCATCGCCTCCCCCACCGACTACCACAACGGCTGCCGCAGCGTGTTGCTGATGGCGTCGCCGACGGAGTAGCAGAAGGGGTGGCGGAGGGr5r6r!r"r%r(r'r&r>r=rrrrrr)r,r+r*r rrr7rr.r/r0r-rrr3r2r4r1rArDrCrBrrr rrr r r r rrr;r:r<r9r@r?r8rrrrr$r#rr)ZCYSZASPZSERZGLNZMETZASNZPROZLYSZSTOPZTHRZPHEZALAZGLYZILEZLEUZHISZARGZTRPZVALZGLUZTYRc@s@eZdZdZddZddZddZdd Zd d Zd d Z dS)CodonAdaptationIndexaOA 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. cCsi|_i|_dS)zInitialize the class.N)index codon_count)selfrI6lib/python3.7/site-packages/Bio/SeqUtils/CodonUsage.py__init__IszCodonAdaptationIndex.__init__cCs ||_dS)zSet up an index to be used when calculating CAI for a gene. Just pass a dictionary similar to the SharpEcoliIndex in the CodonUsageIndices module. N)rF)rHrFrIrIrJ set_cai_indexOsz"CodonAdaptationIndex.set_cai_indexc Cs|jiks|jikrtd||xtD]}d}g}t|}x|D]}||j|7}qFWx0|D](}t|t|}||j||qbWt|}x&t |D]\} }|| ||j|<qWq,WdS)aGenerate 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. RCSU values zVan index has already been set or a codon count has been done. Cannot overwrite either.gN) rFrG ValueError _count_codonsSynonymousCodonsfloatlenappendmax enumerate) rH fasta_fileZaaZtotalZrcsuZcodonscodon denominatorZrcsu_maxZ codon_indexrIrIrJgenerate_indexWs     z#CodonAdaptationIndex.generate_indexcCsd\}}|jikr|t|r,|}xrtdt|dD]^}|||d}||jkr|dkr|t|j|7}|d7}q>|dkr>t d||jfq>Wt ||dS) zCalculate 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. )rrr)rr8r)r7rrz!illegal codon in sequence: %s. %sg?) rFrLrislowerupperrangerQmathlog TypeErrorZexp)rH dna_sequenceZ cai_valueZ cai_lengthirVrIrIrJ cai_for_genes    z!CodonAdaptationIndex.cai_for_genec Cst|}t|_xt|dD]}t|jrDt|j }n t|j}xXt dt |dD]D}|||d}||jkr|j|d7<q`t d||j fq`Wq"WWdQRXdS)NZfastarrYrzillegal codon %s in gene: %s)open CodonsDictcopyrGrparsestrseqrZr[r\rQr_id)rHrUZhandleZ cur_recordr`rarVrIrIrJrNs    z"CodonAdaptationIndex._count_codonscCs.x(t|jD]}td||j|fq WdS)zbPrint out the index used. This just gives the index when the objects is printed. z%s %.3fN)sortedrFprint)rHrarIrIrJ print_indexsz CodonAdaptationIndex.print_indexN) __name__ __module__ __qualname____doc__rKrLrXrbrNrlrIrIrIrJrE?s)rE) rpr]ZCodonUsageIndicesrZBiorrdrOrErIrIrIrJsR