ó jF‰\c@ sYddlmZddlZddlZddlZddlmZm Z m Z idd6dd6dd6dd6dd 6d d 6d d 6dd6dd6dd6dd6dd6dd6dd6dd6Z ej e ƒjZdded„Zd d!„Zdd"„Zdd#„Zdd$„Zdd%„Zd&„Zd'„Zd(„Zd)d*„Zd+d,d-„ZdS(.iÿÿÿÿ(tdivisionN(tvalidate_matrixtvalidate_probability_mattvalidate_information_mattAtCtGtTtAGtRtCTtYtGCtStATtWtGTtKtACtMtCGTtBtAGTtDtACTtHtACGtVtACGTtNic C s–ddddh}dddh}t|ƒ}||krH|jƒ}n ||ksdtd|ƒ‚||ks€td|ƒ‚|dkrË|dkrªt||ƒ}qU|dkrUt||ƒ}qUnŠ|dkrét||ƒ} nN|dkrt||ƒ} n0|dkr%t||ƒ} nts7tdƒ‚t | ddd |d |ƒ}|r†|dkswtd d ƒ‚t |ƒ}nt|ƒ}|S( s¿ Transforms a matrix of one type into a matrix of another type. i = position c, d = character l = pseudocount C = number of characters N_ic = counts matrix element P_ic = probability matrix element Q_ic = background probability matrix element W_ic = weight matrix element I_ic = information matrix element counts -> probability: P_ic = (N_ic + l)/(N_i + C*l), N_i = sum_c(N_ic) probability -> weight: W_ic = log_2(P_ic / Q_ic) weight -> probability: P_ic = Q_ic * 2^(W_ic) probability -> information: I_ic = P_ic * sum_d(P_id * log2(P_id / W_id)) information -> probability: P_ic = I_ic / sum_d(I_id) parameters ---------- df: (dataframe) The matrix to be transformed. from_type: (str) Type of input matrix. Must be one of 'counts', 'probability', 'weight', or 'information'. to_type: (str) Type of output matrix. Must be one of 'probability', 'weight', or 'information'. Can NOT be 'counts'. background: (array, or df) Specification of background probabilities. If array, should be the same length as df.columns and correspond to the probability of each column's character. If df, should be a probability matrix the same shape as df. pseudocount: (number >= 0) Pseudocount to use when transforming from a count matrix to a probability matrix. center: (bool) Whether to center the output matrix. Note: this only works when to_type = 'weight', as centering a matrix doesn't make sense otherwise. returns ------- out_df: (dataframe) Transformed matrix tcountst probabilitytweightt informationsError: invalid from_type=%ssError: invalid to_type="%s"sTHIS SHOULD NEVER HAPPENt from_typetto_typet backgrounds6Error: the option center=True is only compatible with sto_type == "weight"( RtcopytAssertionErrort_probability_mat_to_weight_matt#_probability_mat_to_information_matt_counts_mat_to_probability_matt_weight_mat_to_probability_matt#_information_mat_to_probability_mattFalsettransform_matrixt center_matrix( tdfR"R#R$t pseudocounttcentert FROM_TYPEStTO_TYPEStout_dftprob_df((s../../logomaker/src/data.pyR-!s@E              gð?cC s›|dkstdƒ‚t|ƒ}|jƒ}|j|}||jddƒdd…tjf|jdd…dd…f= 0. taxisiN( R&RR%tvaluestsumtnptnewaxistloctnormalize_matrixR(R/R0R4tvals((s../../logomaker/src/data.pyR)£s   B  cC stt|ƒ}t||ƒ}|jƒ}tj|tƒtj|tƒ|jdd…dd…fR%R7R9tpowerR;R<R(R/R$RAR4((s../../logomaker/src/data.pyR*Ìs  5  cC s¹t|ƒ}t||ƒ}|jƒ}|j}|j}|tj|tƒtj|tƒ}|jddƒ}||dd…tjf|j dd…dd…fR%R7R9R?R@R8R:R;R(R/R$RAR4tfg_valstbg_valsttmp_valstinfo_vec((s../../logomaker/src/data.pyR(äs    (6 cC s(t|ƒ}t|ƒ}t|ƒ}|S(s@ Converts a probability matrix to an information matrix (RR<R(R/R$R4((s../../logomaker/src/data.pyR+ýs   cC sÂt|ƒ}t|jjƒdkƒs3tdƒ‚|jddƒj}ttj|dƒƒ smtdƒ‚|j ƒ}|j|dd…tj f|j dd…dd…f out_df represents a uniform background 2. background is a vector => this vector is normalized then used as the entries of the rows of out_df 3. background is a dataframe => it is then normalized and use as out_df iNs4Error: df and background have mismatched dimensions.s,Error: df and bg_mat have different indexes.s,Error: df and bg_mat have different columns.(tshapeR%tNoneR;t isinstanceR9tndarraytlistttupletarraytlenR&R:R<tpdtcoretframet DataFrameRRGtindextcolumnsR(R/R$tnum_postnum_colsR4((s../../logomaker/src/data.pyR>>s(   & 2     Rc K s»t|ƒ}tdƒ}tt|ƒƒ}tjddd|d|ƒ}xNtt|ƒƒD]:\}}t|} x!| D]} d|j|| f  (t __future__RtnumpyR9tpandasRVtpdbtlogomaker.src.validateRRRRatfinfoRottinyR@ROR,R-R)R'R*R(R+R<R.R>RkRv(((s../../logomaker/src/data.pytsF             , *