ó
ü™Ic        
   @   sý  y d  d l  m Z Wn- e k
 rC d  d l m Z e d ƒ ‚ n Xd  d l m Z d „  Z d GHd d d	 d
 g Z d d d d g Z dW dX dY dZ g Z	 d GHe j
 e e e	 ƒ Z d GHe j e d ƒ Z x) e D]! \ Z Z d e e ƒ e f GHqÐ We e ƒ d GHd d g Z d d d  g Z d[ g Z d GHd$ d% g Z d& d' g d( d( g g Z d) d* d' g d* d& d+ g g Z e e ƒ e e ƒ Z Z e j e e e d, e d- e d. e ƒZ e \ Z Z Z e j e e e e e ƒ Z e e ƒ d/ d\ d0 „  ƒ  YZ e ƒ  Z e j d1 d2 d1 d2 d3 g d3 d4 d3 d4 d2 g d5 ƒ GHe j d6 d7 d8 d2 d9 g d: d; d6 d< d= g d> ƒ GHe j d? d@ dA dB d= g dC dD dE dF d= g dG ƒ GHe j dH dI d" dJ d? g dK dL d: dM d; g dN ƒ GHe j dO dP dQ dR dM g dS dB dT dU d= g d ƒ GHdV S(]   iÿÿÿÿ(   t   asarray(   t   MissingExternalDependencyErrors1   Install NumPy if you want to use Bio.MarkovModel.(   t   MarkovModelc         C   s@  d d j  |  j ƒ GHd d j  |  j ƒ GHd GHx: t t |  j ƒ ƒ D]# } d |  j | |  j | f GHqE Wd GHx` t t |  j ƒ ƒ D]I } g  |  j | D] } d | ^ q› } d |  j | d j  | ƒ f GHq‡ Wd	 GHx` t t |  j ƒ ƒ D]I } g  |  j | D] } d | ^ q} d |  j | d j  | ƒ f GHqï Wd  S(
   Ns
   STATES: %st    s   ALPHABET: %ss   INITIAL:s
     %s: %.2fs   TRANSITION:s   %.2fs     %s: %ss	   EMISSION:(   t   joint   statest   alphabett   ranget   lent	   p_initialt   p_transitiont
   p_emission(   t   markov_modelt   it   x(    (    s   test_MarkovModel.pyt   print_mm
   s    $#$s   TESTING train_visiblet   0t   1t   2t   3t   At   Ct   Gt   Tt   AACCCGGGTTTTTTTt   001112223333333t   ACCGTTTTTTTt   01123333333t   ACGGGTTTTTTt   01222333333t   ACCGTTTTTTTTt   011233333333s   Training HMMt   Classifyingt   AACGTTs   State %s, %0.10fs   TESTING baum welcht   CPt   IPt   colat   ice_tt   lemi   i   i    g      ð?gH¯¼šò×z>gffffffæ?g333333Ó?g      à?g333333ã?gš™™™™™¹?gš™™™™™É?R	   R
   R   t	   DNAStrandc           B   s   e  Z d  „  Z RS(   c         C   s8  d } d } g  | D] } t  | ƒ d ^ q } g  | D] } t  | ƒ d ^ q6 } d d g } t | ƒ } g  } | j d | d | d g ƒ | j | d d | d g ƒ t | ƒ } g  }	 |	 j | d  ƒ |	 j | d  ƒ t |	 ƒ }	 t j | | | | |	 ƒ }
 t j |
 | ƒ } | d \ } } d	 j | ƒ S(
   Nt   NRt   AGTCid   g      ð?g        iÿÿÿÿi   i    t    (   t   floatR    t   appendR   t   find_statesR   (   t   selft   normalt   islandt	   dnastrandR   R   R   R	   R
   R   t   mm(    (    s   test_MarkovModel.pyt
   mostLikely‚   s&    ##(   t   __name__t
   __module__R3   (    (    (    s   test_MarkovModel.pyR'      s   i   i   i
   i(   t   TGCCi   i   i>   i,   i'   i   i*   i   t   CCTGAGTTAGTCGTi-   i$   i   i   i   i   i   i.   t   CCGTACTTACCCAGGACCGCAGTCCiK   i   i   i"   i   i   t   TTAGCAGTGCGi   i%   i   i   i   i!   i   N(   R   R   (   R   R   (   R   R   (   R   R   (   i   i   i    (    (   t   numpyR    t   ImportErrort   BioR   R   R   R   R   t   training_datat   train_visibleR2   R-   t
   state_listt   state_floatt   reprt   outputsR	   R
   R   R   t   Nt   Mt   _baum_welchR   R'   t   dsR3   (    (    (    s   test_MarkovModel.pyt   <module>   sr   		
			
7	