ó
¿MT]c        	   @   sÀ   d  d l  Z  d  d l Z d  d l Z d  d l Z d  d l Z d d l m Z d d l	 m
 Z
 d d l Td d l Td d l Td „  Z d d d	 d d
 d „ Z d
 d d d	 d d d d d „ Z d S(   iÿÿÿÿNi   (   t	   Joint_MDS(   t   calculate_compartment_fraction(   t   *c
         C   s«   t  |  | | | | ƒ }
 t  | | |	 | | ƒ } t d | d d d t d t j j ƒ  d t j j ƒ  d d d	 d
 d | ƒ j |
 | ƒ \ } } | j | ƒ | j | ƒ d S(   s'   Infers 3D coordinates for one structuret   pt   n_componentsi   t   metrict   random_state1t   random_state2t   verbosei    t   dissimilarityt   precomputedt   n_jobsN(   t   distmatR    t   Truet   npt   randomt   RandomStatet   fit_transformt	   setCoords(   t   path1t
   structure1t   path2t
   structure2t   alphat   penaltyt   num_threadst   weightt   size1t   size2t   distMat1t   distMat2t   coords1t   coords2(    (    s   multimds/multimds.pyt   infer_structures   s
    ]i   gš™™™™™©?i   t    c         C   sÁ  t  |  ƒ } t  | ƒ } t |  | ƒ }	 t | | ƒ }
 t |	 |
 f ƒ t |  |	 | |
 | | | | | | ƒ
 t j j t j j |  ƒ ƒ d } |	 j d j	 | | ƒ ƒ t j j t j j | ƒ ƒ d } |
 j d j	 | | ƒ ƒ t
 |	 |
 ƒ } t d j	 | | | ƒ d ƒ ˆ } xt t |	 j ƒ  | ƒ D]] \ } } | j d j |	 j j t | ƒ t | |	 j j ƒ t | ƒ f ƒ ƒ | j d ƒ q'W| j ƒ  Wd QXd GHt |	 |
 |  | | | ƒ GH|	 |
 f S(	   s   MDS without partitioningi    s   {}{}_structure.tsvs   {}{}_{}_relocalization.bedt   ws   	s   
Ns   Fractional compartment change: (   t   size_from_bedt   structureFromBedt   make_compatibleR!   t   ost   patht   splitextt   basenamet   writet   formatt   calculate_distancest   opent   zipt   getGenCoordst   joint   chromt   namet   strt   rest   closeR   (   R   R   R   R   R   R   t   prefixR   R   R   R   t   prefix1t   prefix2t   distst   outt	   gen_coordt   dist(    (    s   multimds/multimds.pyt   full_mds   s&    %""!"Di Hèi
   c
   1      C   s/  t  |  ƒ }
 t  | ƒ } t |  ƒ } t | ƒ } t | | f ƒ } | j | ƒ } t |  |
 | ƒ } t | | | ƒ } t | | f ƒ t | j ƒ  ƒ } | | d k  s­ t ‚ t	 | | ƒ } t
 j g  t | ƒ D]+ } | | t | d | | d ƒ f ^ qÐ ƒ } t | | ƒ t | | ƒ g  } g  } | j ƒ  } d } d } x¨ | D]  } | | d } | | d } t |  |
 | | | | ƒ } t | | | | | | ƒ } | j | ƒ | j | ƒ | t | j ƒ d 7} | t | j ƒ d 7} qIWx- t | | ƒ D] \ } } t | | f ƒ qýWt g  | | d ƒ }  t g  | | d ƒ }! t |  | | | | | | |	 |
 | ƒ
 d GHt j j |  j ƒ }" t j j |! j ƒ }# t j j | j ƒ }$ t j j | j ƒ }% t |  j ƒ }& t | t j ƒ  |& f ƒ } t j | ƒ « }' x¡ |' j |& ƒ D] }( |" |( }) |# |( }* t |  |) | |* d | | |	 |
 | ƒ
 t |$ |( |) | ƒ t |% |( |* | ƒ |) |" |( <|* |# |( <d j |( d |& ƒ GHqWWd QX|  j |" ƒ |! j |# ƒ |  j  ƒ  |! j  ƒ  t! j" j# t! j" j$ |  ƒ ƒ d }+ |  j% d j | |+ ƒ ƒ t! j" j# t! j" j$ | ƒ ƒ d }, |! j% d j | |, ƒ ƒ t& |  |! ƒ }- t' d	 j | |+ |, ƒ d
 ƒ ˆ }. xt t |  j ƒ  |- ƒ D]] \ }/ }0 |. j% d j( |  j) j* t+ |/ ƒ t+ |/ |  j) j, ƒ t+ |0 ƒ f ƒ ƒ |. j% d ƒ q•W|. j- ƒ  Wd QXd GHt. |  |! |  | |
 | ƒ GH|  |! f S(   s8   Partitions structure into substructures and performs MDSi   i   i    s   Low-resolution MDS completeg      @s#   MDS performed on structure {} of {}Ns   {}{}_structure.tsvs   {}{}_{}_relocalization.bedR#   s   	s   
s   Fractional compartment change: (/   R$   t   chromFromBedt   consensus_chromt	   reduceResR%   R&   t   lent	   getPointst   AssertionErrort   intR   t   arrayt   ranget   mint   substructuresFromAbsoluteTadsR0   t   appendt   pointsR/   t   make_points_compatiblet	   StructureR!   t   pympt   sharedt   listt
   structurest   mpt	   cpu_countt   Parallelt	   transformR,   t   setstructurest   set_rel_indicesR'   R(   R)   R*   R+   R-   R.   R1   R2   R3   R4   R5   R6   R   (1   R   R   R7   t   num_partitionst	   maxmemoryR   R   t	   res_ratioR   R   R   R   t
   highChrom1t
   highChrom2t	   highChromt   lowChromt   lowstructure1t   lowstructure2t   nt   partition_sizet   it   lowpartitionst   high_substructures1t   high_substructures2t   low_gen_coordst   offset1t   offset2t	   partitiont   start_gen_coordt   end_gen_coordt   high_substructure1t   high_substructure2t   highstructure1t   highstructure2t   highSubstructures1t   highSubstructures2t   lowSubstructures1t   lowSubstructures2t   numSubstructuresR   t   substructurenumt   highSubstructure1t   highSubstructure2R8   R9   R:   R;   R<   R=   (    (    s   multimds/multimds.pyt   partitioned_mds2   sˆ    G%

%



""!"D(   t   syst   numpyR   RN   t   multiprocessingRR   R'   t	   joint_mdsR    t   compartment_analysisR   t
   data_toolst   linear_algebrat   tadR!   R>   Ry   (    (    (    s   multimds/multimds.pyt   <module>   s   


	
