ó ü Ic@sÃdZddlZd„ZejjƒdZejeƒZddd„ƒYZd„Z d„Z d „Z ddddd „Z d Zdddddddd „Zd „Zd„Zd„Zdddd„Zd„Zdd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zyddl Z Wne!k reZ"nZXddl#Z#e#j$e%Z&x=e j'j(ƒD],Z)e)j*dƒse j'e)e&j'e) MarkovModel()sSTATES:is ALPHABET:sINITIAL:s %s:iÿÿÿÿs TRANSITION:Ns EMISSION:( RtsplitR RtnumpytzerosR trangetfloatR tmapR(RRR R tmmtNtMti((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MarkovModel.pytload7s,!00cCsU|j}|ddj|jƒƒ|ddj|jƒƒ|dƒx?tt|jƒƒD](}|d|j||j|fƒq]W|dƒxWtt|jƒƒD]@}tt |j|ƒ}|d|j|dj|ƒfƒq©W|dƒxWtt|j ƒƒD]@}tt |j |ƒ}|d|j|dj|ƒfƒq Wd S( ssave(mm, handle)s STATES: %s t s ALPHABET: %s s INITIAL: s %s: %g s TRANSITION: s %s: %s s EMISSION: N( twritetjoinR R R#RR R R%tstrR(R&RtwR)tx((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MarkovModel.pyR[s  & ( c Cs¶t|ƒt|ƒ}}|s.tdƒ‚n|d krjt|ƒ}|j|fkrjtdƒ‚qjn|d kr­t|ƒ}|j||fkr­tddƒ‚q­n|d krðt|ƒ}|j||fkrðtddƒ‚qðng} t|ƒ} x2|D]*} | jg| D]} | | ^qƒq Wtt| ƒ} t| ƒdkrgtdƒ‚nt ||| d |d |d |d |ƒ} | \}}}t |||||ƒS(s^train_bw(states, alphabet, training_data[, pseudo_initial] [, pseudo_transition][, pseudo_emission][, update_fn]) -> MarkovModel Train a MarkovModel using the Baum-Welch algorithm. states is a list of strings that describe the names of each state. alphabet is a list of objects that indicate the allowed outputs. training_data is a list of observations. Each observation is a list of objects from the alphabet. pseudo_initial, pseudo_transition, and pseudo_emission are optional parameters that you can use to assign pseudo-counts to different matrices. They should be matrices of the appropriate size that contain numbers to add to each parameter matrix, before normalization. update_fn is an optional callback that takes parameters (iteration, log_likelihood). It is called once per iteration. sNo training data given.s$pseudo_initial not shape len(states)spseudo_transition not shape slen(states) X len(states)spseudo_emission not shape slen(states) X len(alphabet)is,I got training data with outputs of length 0tpseudo_initialtpseudo_transitiontpseudo_emissiont update_fnN( RRRtasarraytshapeRtappendR%tmint _baum_welchR (R R t training_dataR1R2R3R4R'R(ttraining_outputstindexestoutputsR0tlengthsR 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/MarkovModel.pyttrain_bwns>        ( ièc  Csÿ|dkrt|ƒ}nt||fƒ}|dkrNt||fƒ}nt|||fƒ}|dkr„t||fƒ}nt|||fƒ}ttj|||fƒ\} } } |dkrÛtj|ƒ} nd} |dkrÿtj|ƒ}nd}|dkr#tj|ƒ}nd}d}x´ttƒD]–}t}x<|D]4}t |||| | | | ||ƒ }||7}qOW| dk r£| ||ƒn|dk rÌtj ||ƒdkrÌPn|}q<Wt dtƒ‚ttj | | | fƒS(Ngš™™™™™¹?s%HMM did not converge in %d iterations( Rt _random_normt_copy_and_checkR%R!tlogR#tMAX_ITERATIONStLOG0t_baum_welch_onetfabst RuntimeErrortexp(R'R(R;R R RR1R2R3R4t lp_initialt lp_transitiont lp_emissiontlpseudo_initialtlpseudo_transitiontlpseudo_emissiont prev_llikR)tllikR=R0((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MarkovModel.pyR9®sJ   !       %  c  Cs³t|ƒ} t|| ||||ƒ} t|| |||ƒ} tj||| fƒ} xÎt| ƒD]À} || }tj||fƒ}xot|ƒD]a}xXt|ƒD]J}| || ||||||| || d}|||| MarkovModel Train a visible MarkovModel using maximum likelihoood estimates for each of the parameters. states is a list of strings that describe the names of each state. alphabet is a list of objects that indicate the allowed outputs. training_data is a list of (outputs, observed states) where outputs is a list of the emission from the alphabet, and observed states is a list of states from states. pseudo_initial, pseudo_transition, and pseudo_emission are optional parameters that you can use to assign pseudo-counts to different matrices. They should be matrices of the appropriate size that contain numbers to add to each parameter matrix s$pseudo_initial not shape len(states)spseudo_transition not shape slen(states) X len(states)spseudo_emission not shape slen(states) X len(alphabet)sstates and outputs not alignedN( RRR5R6RRR7t_mleR (R R R:R1R2R3R'R(ttraining_statesR;tstates_indexestoutputs_indexesttoutputsttstatesR0R 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/MarkovModel.pyt train_visiblebs6         $(cCs6tj|ƒ}|r"||}nx"|D]}||dcd7 list of (states, score)(RR R tVERY_SMALL_NUMBERR RR%R!RBRR t_viterbiR#RH(t markov_modeltoutputR&R'R0tytzRIRJRKR<tresultsR)R tscore((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MarkovModel.pyt find_statesÀs   $7cCst|ƒ}g}x(t|ƒD]}|jdg|ƒqWtj||fƒ}||dd…|df|dd…df 2 dimensions( R!tarrayR6t ValuErrorRRFRlRR#(Rbt desired_shapeR)((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MarkovModel.pyRAs# cCsf||dkr|S||dkr(|St||ƒ}|tjtj||ƒtj||ƒƒS(Nid(R8R!RBRH(tlogxtlogytminxy((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MarkovModel.pyRU)s cCsit|jƒdkr9tj|tj|jƒfƒ}n|}t}x|D]}t||ƒ}qLW|S(Ni(RR6R!treshapetproductRDRU(RbtvecRltnum((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MarkovModel.pyRS1s$ cCsut|ƒt|ƒks$tdƒ‚tjt|ƒƒ}x5tt|ƒƒD]!}t||||ƒ||sR     $   = 8 R   4 %   ,