ó jëIc@shdZddlmZddlmZddlmZddlZddlZde fd„ƒYZ dS(s€ Implementation of sequence motifs. Changes: 10.2007 - BW added matrix (vertical, horizontal) input, jaspar, transfac-like output 26.08.2007 - added a background attribute (Bartek Wilczynski) 26.08.2007 - added a DPQ measure (Bartek Wilczynski) 9.2007 (BW) : added the .to_fasta() and .weblogo() methods allowing to use the Berkeley weblogo server at http://weblogo.berkeley.edu/ iÿÿÿÿ(tSeq(t FreqTable(tIUPACNtMotifcBsÁeZdZejd„Zd„Zd„Zd„Zd„Z e d„Z e d„Z d„Z ed „Zd „Zd d d „Zd d d e d„Zd d„Zd„Zd„Zd„Zd„Zd„Zd„Zed„Zd„Zd„Zd„Zd„Zed„Zd-ed„Z!d-ed„Z"d„Z#d„Z$d „Z%d!„Z&d"„Z'd#„Z(d$„Z)d%„Z*d&d'„Z+d(„Z,d-d)„Z-d-e d*„Z.d+„Z/d,„Z0RS(.s/ A class representing sequence motifs. cs©gˆ_tˆ_iˆ_tˆ_gˆ_tˆ_gˆ_tˆ_gˆ_ |ˆ_ dˆ_ t t‡fd†ˆj jƒƒˆ_dˆ_dˆ_dˆ_dS(Ncs|dtˆjjƒfS(Ngð?(tlentalphabettletters(tn(tself(sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt#sgð?t(t instancestFalset has_instancestcountst has_countstmaskt_pwm_is_currentt_pwmt_log_odds_is_currentt _log_oddsRtNonetlengthtdicttmapRt backgroundtbetatinfotname(RR((Rsƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt__init__s           '  cCsP|jdkr||_n1|j|krLdG|jG|jGHtdƒ‚ndS(NRs(You can't change the length of the motif(RRR t ValueError(RR((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt _check_length(s  cCs=|jdkr||_n|j|kr9tdƒ‚ndS(NsWrong Alphabet(RRR(RR((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt_check_alphabet/s cCs¯|j|jƒ|jt|ƒƒ|jrjx;t|jƒD]'}||}|j||cd7 instance %d s (R tmake_instances_from_countst enumerateR R@(RR€R%R((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt _to_fastas    cCsõtƒ}|jr<xÐ|jD]}|j|jƒƒqWn©t|_|jd|jd<|jd|jd<|jd|jd<|jd|jd<|jdjƒ|jdjƒ|jdjƒ|jdjƒ|j |_ |j |_ |S(s; Gives the reverse complement of the motif tTtAtCtG( RR R R'RLR#RRtreverseRR(RR7R%((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyRL™s      cCs|j|ddd|ƒS(sq reads the motif from Jaspar .pfm file The instances are fake, but the pwm is accurate. RtACGTtmake_instances(t_from_horiz_matrix(RR}R((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt_from_jaspar_pfm°sc Csúi|_t|_|dkr-|jj}nd|_x|D]}g|j|Creates the count matrix for a motif with instances. cSs |dfS(Ni((R5((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyR si( RRR#RRR R!RRRR"R(RRR5RjR%tciR((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pytmake_counts_from_instancess  cCsxétrë|jƒ}|dks1|ddkr5Pn|jƒjƒ}d}x(||||jƒkrw|d7}qPWd}xH|t|ƒkrÈ||||jƒkrÈ|||7}|d7}qWt||jƒ}|j|ƒqW|j dt|ƒƒ|S(s` reads the motif from Jaspar .sites file The instances and pwm are OK. R it>iR(( R#R{R|tlowerRRMRRR'R+(RR}R~R%R((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt_from_jaspar_sitess   /cCs.|t|jƒkr#|jƒ|S|jSdS(sËReturns the probability distribution over symbols at a given position, padding with background. If the requested index is out of bounds, the returned distribution comes from background. N(R!RR1R(Rtindex((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt __getitem__7scCsŒd}xst|jƒD]b}d}d}xC||jƒD]1}||||kr9|||}|}q9q9W||7}qWt||jƒS(s3Returns the consensus sequence of a motif. R itX(R!RtkeysRR(RR7R%tmax_ftmax_nR((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt consensusAs cCsŒd}xst|jƒD]b}d}d}xC||jƒD]1}||||kr9|||}|}q9q9W||7}qWt||jƒS(sLreturns the least probable pattern to be generated from this motif. R g$@R¦(R!RR§RR(RR7R%tmin_ftmin_nR((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt anticonsensusOs cCs|j|jƒdƒS(soMaximal possible score for this motif. returns the score computed for the consensus sequence. i(RKRª(R((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt max_score]scCs|j|jƒdƒS(ssMinimal possible score for this motif. returns the score computed for the anticonsensus sequence. i(RKR­(R((sƒ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/_Motif.pyt min_scoredstPNGcKsœddl}ddl}|jƒ}d}i|d6|d6dd6dd 6d d 6d d 6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd 6dd!6dd"6d#d$6dd%6dd&6d'd(6d)d*6d+d,6d-d.6d/d06d1d26d3d46d/d*6}x*|jƒD]\} } t| ƒ|| s