B b#P@sdZddlZy ddlZWn(ek r@ddlmZedYnXddlmZddl m Z Gdd d e Z Gd d d e Z Gd d d e ZGddde ZdS)zSupport for various forms of sequence motif matrices. Implementation of frequency (count) matrices, position-weight matrices, and position-specific scoring matrices. N)MissingPythonDependencyErrorz3Install NumPy if you want to use Bio.motifs.matrix.)Seq)_pwmc@s`eZdZdZddZddZddZedd Zed d Z ed d Z eddZ ddZ dS)GenericPositionMatrixz9Base class for the support of position matrix operations.cCsbd|_xP|D]H}|jdkr*t|||_n|jt||krDtdt||||<q W||_dS)zInitialize the class.Nzdata has inconsistent lengths)lengthlen Exceptionlistalphabet)selfr valuesletterr0lib/python3.7/site-packages/Bio/motifs/matrix.py__init__!s  zGenericPositionMatrix.__init__cCsxddt|jD}dd|}|g}x<|jD]2}dd||D}d|d|}||q0Wd|d}|S)zPReturn a string containing nucleotides and counts of the alphabet in the Matrix.cSsg|] }d|qS)z%6dr).0irrr .sz1GenericPositionMatrix.__str__..z  cSsg|] }d|qS)z%6.2fr)rvaluerrrr2sz%c:  )rangerjoinr append)r Zwordslinelinesrtextrrr__str__,s zGenericPositionMatrix.__str__csRt|tr>t|dkr|\}}t|trf|tj\}}}t|||}fdd|D}d} nrt|trj|} d} nXt|trfdd|D}d} n6t|trt|dkr|} d} qt |n t d|t|tr|j \} } } t| | | }d}n"t|tr|}d}n t d|| dkrN|dkrNt | |S| dkr|dkrt | tfdd|DS| dkr|dkri}x"|D]} t | ||| <qW|Si}x0|D](} t | fd d|D|| <qWt |jkrj|S|Sn t|dkr6|d }nt d t|tr|tj\}}}t|||}fd d|D}d}nzt|trj|}d}n^t|trćfd d|D}d}n:t|trt|dkr|}d}nt |n t d||dkrt |S|dkrFi}x|D]}t |||<q(W|StddS)z(Return the position matrix of index key.csg|]}j|qSr)r )rr)r rrr@sz5GenericPositionMatrix.__getitem__..rcsg|]}j|qSr)r )rr)r rrrFszCannot understand key %sc3s|]}|VqdS)Nr)rindex2)r rr ]sz4GenericPositionMatrix.__getitem__..csg|] }|qSrr)r_)r rrrgsrz"keys should be 1- or 2-dimensionalcsg|]}j|qSr)r )rr)r rrrsscsg|]}j|qSr)r )rr)r rrryszShould not get hereN) isinstancetuplersliceindicesr rintstrKeyErrorrdict __getitem__sorted __class__ RuntimeError)r keyZkey1Zkey2Zstart1Zstop1Zstride1Zindices1Zletters1Zdim1Zletter1Zstart2Zstop2Zstride2Zindices2Zdim2r dstartstopZstrider&lettersZdimrr)r r rr+8s                               z!GenericPositionMatrix.__getitem__cCs\d}xNt|jD]@}tj }x*|jD] }|||}||kr$|}|}q$W||7}qWt|S)zReturn the consensus sequence.)rrmathinfr r)r sequencerZmaximumrcountsequence_letterrrr consensuss   zGenericPositionMatrix.consensuscCsZd}xLt|jD]>}tj}x*|jD] }|||}||kr"|}|}q"W||7}qWt|S)z"Return the anticonsensus sequence.r4)rrr5r6r r)r r7rZminimumrr8r9rrr anticonsensuss   z#GenericPositionMatrix.anticonsensuscsddddddddd d d d d ddd}d}xtjD]މfdd}t|dd}fdd|D}|dt|ddkr|dd|dkr|d}n`dt|dddt|krdt|dd}n(|ddkrdt|dd}nd}|||}||7}q4Wt|S)z)Return the degenerate consensus sequence.ACGTMRWSYKVHDBN)r<r=r>r?ZACZAGATCGZCTZGTZACGZACTZAGTZCGTACGTr4cs |S)Nr) nucleotide)rr rrgetsz7GenericPositionMatrix.degenerate_consensus..getT)r/reversecsg|]}|qSrr)rc)rr rrrsz>GenericPositionMatrix.degenerate_consensus..rrNrrM)rrr,sumrrOr)r Zdegenerate_nucleotider7rOZ nucleotidescountsr/rNr)rr rdegenerate_consensuss< ,     z*GenericPositionMatrix.degenerate_consensuscCs`|j}d}d}xHt|jD]:}x4|D],}|dkr@||||7}||||7}q$WqW||S)z Compute the fraction GC content.grL)r rr)r r Zgc_totaltotalrrrrr gc_contents z GenericPositionMatrix.gc_contentcCsi}|jdkr<|dddd|d<|dddd|d<n,|dddd|d<|dddd|d<|dddd|d<|dddd|d<|j}|||S) zCompute reverse complement.ZACGUUNr<r?r=r>)r r-)r r r rrrreverse_complements z(GenericPositionMatrix.reverse_complementN) __name__ __module__ __qualname____doc__rrr+propertyr:r;rVrXr[rrrrrs  U   . rc@seZdZdZdddZdS)FrequencyPositionMatrixzGClass for the support of frequency calculations on the Position Matrix.NcCsi}|dkr.xx|jD]}dg|j||<qWnXt|trbxL|jD]}t||g|j||<q@Wn$x"|jD]}t|g|j||<qjWx>t|jD]0}x*|jD] }||||||7<qWqWt|j|S)aCreate and return a position-weight matrix by normalizing the counts matrix. 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A generator function, returning found hits in the given sequence with the pwm score higher than the threshold. rr)ZdtypeN) upperrrrtZaranger[rvwhererur'rZargsortzip)r r7Z thresholdZbothZ chunksizeZseq_lenZmotif_lZ chunk_startsZrcZ chunk_startZsubseqZ pos_scoresZpos_indZ pos_positionsZ neg_scoresZneg_indZ neg_positionsZchunk_positionsZ chunk_scoresorderrrrsearch~s2     z$PositionSpecificScoringMatrix.searchcs@d}j}x0tdjD] |tfdd|D7}qW|S)zoMaximal possible score for this motif. returns the score computed for the consensus sequence. grc3s|]}|VqdS)Nr)rr)positionr rrr!sz4PositionSpecificScoringMatrix.max..)r rrmax)r scorer3r)rr rrs  z!PositionSpecificScoringMatrix.maxcs@d}j}x0tdjD] |tfdd|D7}qW|S)zsMinimal possible score for this motif. returns the score computed for the anticonsensus sequence. grc3s|]}|VqdS)Nr)rr)rr rrr!sz4PositionSpecificScoringMatrix.min..)r rrmin)r rr3r)rr rrs  z!PositionSpecificScoringMatrix.mincCs tddS)zCompute the GC-ratio.z,Cannot compute the %GC composition of a PSSMN)r )r rrrrXsz(PositionSpecificScoringMatrix.gc_contentNc Cs|dkrt|jd}nt|}t|}x|jD]}|||<q4Wd}xrt|jD]d}x^|jD]T}|||f}t|rqht |r|dkrqh||}|t d|}|||7}qhWq\W|S)z.Return expected value of the score of a motif.Ng?grr) r*rer rTr rrr5isnanisinfpow) r rirWrsxrrlrjrkrrrmeans$     z"PositionSpecificScoringMatrix.meanc Cs|dkrt|jd}nt|}t|}x|jD]}|||<q4Wd}xt|jD]}d}d}xn|jD]d}|||f}t|rqpt |r|dkrqp||} | t d|} || |7}|| ||7}qpW|||8}||7}q\Wt |d}t |S)z2Return standard deviation of the score of a motif.Ng?grr) r*rer rTr rrr5rrrrsqrt) r rirWrZvariancerrsxxrlrjrkrrrstds0         z!PositionSpecificScoringMatrix.stdcCsx|j|jkrtdd}xRt|j d|jD]:}|dkrJ||| }n |||}||kr.|}| }q.Wd||fS)zReturn the similarity score based on pearson correlation for the given motif against self. 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