ó
h’<c           @   sU  d  d l  Z  d  d l Z d  d l Z d  d l m Z d  d l m Z m Z e j Z	 e j
 j d d ƒ Z e j e e ƒ ƒ Z e j
 j d d ƒ Z e j e e ƒ ƒ Z e	 j d ƒ e	 j d ƒ x= e j j D]/ Z e	 j d	 e e e e e e ƒ f ƒ qÎ We j
 j d d
 ƒ Z e  j e e ƒ ƒ Z e j e ƒ Z e j e ƒ Z e j e ƒ Z e j  d e	 d d ƒ e	 j d ƒ e j! ƒ  Z" e" j# ƒ  x7 e" D]/ Z e	 j d e e e e e e ƒ f ƒ q˜Wd Z$ e	 j d ƒ e j% ƒ  e j& j! ƒ  Z" e" j# ƒ  x= e" D]5 Z e	 j d e e j& e f ƒ e$ e j& e 7Z$ qWe	 j d e$ ƒ e j' d e d d ƒ Z( e	 j d ƒ e	 j d ƒ e( j  d e	 d d d d ƒ e	 j d ƒ e( j) d e	 d d d d ƒ e	 j d ƒ xJ e j* D]? Z e j e+ e e ƒ ƒ Z, e	 j d e ƒ e, j  d e	 ƒ qàWe	 j d ƒ e( j- e ƒ e	 j d  e( j. ƒ d S(!   iÿÿÿÿN(   t   SubsMat(   t	   FreqTablet
   MatrixInfoR    s   protein_count.txts   protein_freq.txts@   Check differences between derived and true frequencies for each
s)   letter. Differences should be very small
s   %s %f
s   acc_rep_mat.pikt   ft   formats    %4.3fsF   Diff between supplied and matrix-derived frequencies, should be small
s   %s %.2f
g        s<   Calculating sum of letters for an observed frequency matrix
s   %s	%.2f
s   Total sum %.2f should be 1.0
t   acc_rep_matt   round_digiti   s   
Log odds matrix
s   
Log odds half matrix
s    %dt   alphabett   AVILMCFWYHSTNQKRDEGPs   
Log odds full matrix
s   
Testing MatrixInfo
s   
%s
------------
s   
Testing Entropy
s   relative entropy %.3f
(/   t   cPicklet   syst   ost   BioR    t   Bio.SubsMatR   R   t   stdoutR   t   patht   joint	   ftab_filet
   read_countt   opent	   ftab_prott	   ctab_filet	   read_freqt	   ctab_prott   writeR   t   letterst   it   abst   pickle_filet   loadR   t   SeqMatt   _build_obs_freq_matt   obs_freq_matt   _exp_freq_table_from_obs_freqt
   ftab_prot2t	   print_matt   keyst   kst   sortt   st   all_letters_sumt   sum_letterst   make_log_odds_matrixt   lo_mat_prott   print_full_matt   available_matricest   getattrt   matt   make_relative_entropyt   relative_entropy(    (    (    s   test_SubsMat.pyt   <module>   s^   	-
-

