ó š¢Ic@s…ddlmZddlmZddlmZddlZdd d„ƒYZdefd„ƒYZd d d „ƒYZ d „Z dS(iÿÿÿÿ(tSeq(tIUPAC(tsqrtNtMotifcBskeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z d d „Z RS( s´A generic motif class. A Motif has information about the alphabet used in the motif, the length of the motif, the motif name, the number of occurrences, and the individual instances of the motif. Each of the instances is an object of the Instance class. Methods: add_instance(instance): adds a new instance of the motif. get_instance_by_name(name): returns an instance with the specified name. cCsCg|_d|_d|_d|_d|_d|_g|_dS(Nit(t instancestNonetalphabettlengthtnum_occurrencestnamet consensustpssm(tself((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyt__init__s      cCs^t|tƒrZ|jr+|j|jƒn|jrG|j|jƒn|jj|ƒndS(N(t isinstancetInstanceRt_lengthR t _motifnameRtappend(R tinstance((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyt add_instance s   cCs+x$tjD]}|j|kr |Sq WdS(N(tsetRtseqnameR(R R ti((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pytget_instance_by_name(scCsA|tjks-|tjks-|tjkr9||_ndSdS(Niÿÿÿÿ(Rtunambiguous_dnatproteint ambiguous_dnaR(R R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyt _alphabet.s- cCs7t|ƒtkr||_nt|ƒ}||_dS(N(ttypetintR(R R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyR4s  cCs ||_dS(N(R (R R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyt_name;scCs1|jr$tj||jƒ|_n ||_dS(N(RRR (R R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyt _consensus>s cCs7t|ƒtkr||_nt|ƒ}||_dS(N(RRR (R tnumber((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyt_numoccurrencesDs  c Cs²|jdkrtdƒ‚nd}|jtjkr?d}n|jtjkrZd}ng}|jr¥|jdjr¥xI|jdjD]7}g}x|D]}|jdƒqW|j|ƒqŠWxy|jD]n}xet |j ƒD]T}|j|}y|j |ƒ}Wntk r$d}nX|||cd7tsit/( R R4RRRtziptfiltertstrtjoinR ( R R7R tnull_characterR,R-t this_positiontvalst good_valuesR3tletterst my_letter((R7s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pytmake_consensushs$   #( t__name__t __module__t__doc__RRRRRR R!R#R4RD(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyR s         t MEMEMotifcBsSeZdZd„Zdddddd„Zd„Zd „Zd „Zd „ZRS( sA subclass of Motif used in parsing MEME (and MAST) output. This sublcass defines functions and data specific to MEME motifs. This includes the evalue for a motif and the PSSM of the motif. Methods: add_instance_from_values (name = 'default', pvalue = 1, sequence = 'ATA', start = 0, strand = +): create a new instance of the motif with the specified values. add_to_pssm (position): add a new position to the pssm. The position should be a list of nucleotide/amino acid frequencies add_to_logodds (position): add a new position to the log odds matrix. The position should be a tuple of log odds values for the nucleotide/amino acid at that position. compare_motifs (other_motif): returns the maximum correlation between this motif and other_motif cCs,tj|ƒd|_g|_g|_dS(Ng(RRtevalueR tlogodds(R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyR‰s   tdefaultitATAit+cCs–tƒ}|j|ƒ|j|ƒ|j|ƒ|j|ƒ|j|ƒ|jrf|j|jƒn|jr‚|j |jƒn|j j |ƒdS(N( Rt _sequencet_pvaluet_seqnamet_startt_strandRRR RRR(R R tpvalueR'tstarttstrandtinst((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pytadd_instance_from_valuess        cCs7t|ƒtkr||_nt|ƒ}||_dS(N(RtfloatRI(R RI((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyt_evalueœs  cCs|jj|ƒdS(N(R R(R t thisposition((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyt add_to_pssm£scCs|jj|ƒdS(N(RJR(R RZ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pytadd_to_logodds¦sc Csvt|tƒrX|js'tdƒ‚n|js?tdƒ‚nt|jƒ}t|jƒ}d}||kr‡t|j|jƒ}nÍ||krõ||}x´td|ƒD]A}|j|||!}t|j|ƒ}||kr­|}q­q­Wn_||}xRtd|ƒD]A}|j|||!} t| |jƒ}||kr|}qqW|Stj j t t ƒƒdSdS(NsThis motif does not have a PSSMs$The other motif does not have a PSSMi( RRHR R&R*Rt_corrR(tsyststderrtwriteR<tm2( R tmotiftmylentyourlentmyrtdiffRtyourpssmtrtmypssm((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pytcompare_motifs©s4         ( RERFRGRRWRYR[R\Rj(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyRH}s     RcBs_eZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z RS( sHA class describing the instances of a motif, and the data thereof. cCsCd|_d|_d|_d|_d|_d|_d|_dS(NRigð?(RR't sequence_nameRTRSRURt motif_name(R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyRÌs      cCs ||_dS(N(R'(R tseq((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyRNÕscCs ||_dS(N(Rk(R R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyRPØscCs ||_dS(N(Rl(R R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyRÛscCst|ƒ}||_dS(N(RRT(R RT((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyRQÞs cCst|ƒ}||_dS(N(RXRS(R tpval((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyROâs cCst|ƒ}||_dS(N(RXtscore(R Ro((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyt_scoreæs cCs ||_dS(N(RU(R RU((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyRRêscCs ||_dS(N(R(R R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyRís( RERFRGRRNRPRRQRORpRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyRÉs       cCs?d}d}d}d}d}t|dtkƒrItd„|ƒ}nt|dtkƒrttd„|ƒ}nd„}t|ƒ}x_t||ƒD]N\} } || 7}|| 7}||| ƒ7}||| ƒ7}|| | 7}q™W|||d|} |||d||||d|} | t| ƒ} | S(NicSs||S(N((tatb((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyR8ùscSs||S(N((RqRr((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyR8ûscSs||S(N((tt((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyR8üsgð?(RtlisttreduceR*R:R(R3R2tsxtsytsxxtsyytsxytsqRRqRrts1ts2Rh((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyR]ñs*    *((( tBioRt Bio.AlphabetRtmathRR^RRHRR](((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Motif.pyts rL(