ó
Ý1`Zc           @   s]   d  d l  Td  d l Z d  d l Z d  d l m Z d  d l Z d „  Z	 d „  Z
 d „  Z d S(   iÿÿÿÿ(   t   *N(   t	   euclideanc      
   C   se  t  j |  ƒ d } t |  d d  d  … f ƒ } t  j | | d d ƒ }	 g  }
 xK t d | d ƒ D]6 } |
 g  t | d | ƒ D] } | | f ^ q 7}
 qd W| d k  rg  |
 D]I } t |  | d | | d g |  | d | | d g | | ƒ ^ q± }	 nº t j d | ƒ } g  |
 D]U } | j t d |  | d | | d g |  | d | | d g | | f ƒ^ q} t  j	 g  | D] } | j
 ƒ  ^ q„ƒ }	 | j ƒ  | j ƒ  | j ƒ  t |	 d | d | d d  ƒ\ } } } t  j d | | d f ƒ } d } d } x¡ | | k  r°|  | d  d  … f | | d  d	 … f <| | | | d	 f <| | d  d  … f | | d d  d	 … f <| | | | d d	 f <| d 7} | d 7} qWt | ƒ } g  } x’ | D]Š } | j t | ƒ g ƒ | d	 j t  j |  t  j | | k ƒ d d
 d ƒƒ | d	 j t  j | t  j | | k ƒ d d
 d ƒƒ qÊW| | | f S(   Ni    i   i   t	   processest   argst	   nclusterst   npasst	   initialidiÿÿÿÿt   axis(   t   npt   shapet   lent   zerost   ranget   distancet   mpt   Poolt   apply_asynct   arrayt   gett   closet	   terminatet   joint   kmedoidst   Nonet   sett   appendt   intt   meant   where(   t   tRegions_plust   tRegions_minust   kR   t   pseudot   nproct   testt   Nt   Lt   dmt   indst   it   jt   poolt   rest   pt   clusterst   errort   nfoundt   tRegionst   indt   newindt   IDst	   centroidst   ID(    (    sN   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/clusterRegions6.pyt   clusterRegions   s@    	 4Yb(


'&+
7;c         C   sð  |  d }  | d } t  |  ƒ } g  } g  } xt d | ƒ D]õ } | | d k  rµ | g  t d t |  | ƒ ƒ D] } | ^ qo 7} | g  t d t | | ƒ ƒ D] } | ^ qŸ 7} q< | g  t d t |  | ƒ ƒ D] } | t | d ƒ ^ qÒ 7} | g  t d t | | ƒ ƒ D] } | t | d ƒ ^ q7} q< Wg  t d t | d ƒ d ƒ D] } | ^ qS}	 t j t j | d |	 ƒd t j | d |	 ƒd g ƒ }
 | d k rËt j |
 d |
 d | ƒ d S| d k rìt |
 d |
 d ƒ Sd  S(   Ni    i   i   t   binst   gt   euc(	   R
   R   R   R   R   t	   histogramt   att   gtestR   (   t   p1t   p2R    R"   R#   t   p1_post   p2_posR'   R(   R6   t   contig(    (    sN   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/clusterRegions6.pyR   K   s"    

03>B0;  c         C   s   t  |  | ƒ S(   N(   R   (   R<   R=   (    (    sN   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/clusterRegions6.pyt
   e_distancej   s    (   t   Bio.Clustert   numpyR   t   multiprocessingR   t   scipy.spatial.distanceR   t   analyzeTransitions6_symmetricR:   R5   R   RA   (    (    (    sN   /oak/stanford/groups/akundaje/marinovg/programs/PeakXus/src/clusterRegions6.pyt   <module>   s   
	9	