ó
?îec           @   sÆ   d  d l  Z d  d l m Z d  d l j Z d  d l j Z d  d l	 m
 Z
 d  d l Z e j d i e j ƒ  d 6ƒ d  d l m Z d d d „  ƒ  YZ d	 e f d
 „  ƒ  YZ d e f d „  ƒ  YZ d S(   iÿÿÿÿN(   t   signal(   t   InsertionTrackt
   setup_argst   include_dirs(   t   makeFragmentMatt
   ChunkMat2Dc           B   sn   e  Z d  Z d „  Z d d d d e d „ Z d „  Z d „  Z e	 d „  ƒ Z
 d „  Z d d d d d „ Z RS(	   sT   Class that stores fragments in 2D matrix according to
    center position and lengthc         C   si   | |  _  | |  _ | |  _ | |  _ | |  _ | | |  _ | | |  _ t j |  j |  j f ƒ |  _	 d  S(   N(
   t   chromt   lowert   uppert   startt   endt   ncolt   nrowt   npt   zerost   mat(   t   selfR   R	   R
   R   R   (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt   __init__   s    					c         C   s  | d k r |  j } n  | d k r0 |  j } n  | d k rH |  j } n  | d k r` |  j } n  | |  j } | |  j } | |  j } | |  j }	 | sÔ y! |  j | | … | |	 … f SWqt d ƒ ‚ qXnA| d k  s|	 |  j j d k s| d k  s| |  j j d k r't d ƒ ‚ n  |	 | }
 |
 d d k rPt d ƒ ‚ nÅ t j	 | | |
 f ƒ } x¥ t
 | | ƒ D]” } | |  j d d k rÏ|  j | | |	 … f d d d … | | d d … f <qy|  j | | d |	 … f d d d … d | | d d … f <qyW| Sd S(   sv   get a subset (or all) of the matrix stored by ChunkMat2D object based on
        chromosal position and/or insert sizes6   Looks like dimensions from get probaby don't match Mati   i    i   s&   Can only flip mat if the width is odd!Niÿÿÿÿ(   t   NoneR   R   R	   R
   R   t	   Exceptiont   shapeR   R   t   range(   R   R   R   R	   R
   t   flipt   y1t   y2t   x1t   x2R   t   newt   j(    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt   get   s8    !D
9Bc         C   s1   | j  |  j j  k r$ t d ƒ ‚ n  | |  _ d S(   s   assign a matrix to objects*   Dimensions of input mat are wrong.  Uh oh!N(   R   R   R   (   R   R   (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt   assign7   s    c         C   sY   d j  t t |  j |  j |  j |  j |  j g ƒ ƒ } t j	 | |  j
 d d d | ƒd S(   s   Save object in a text filet   ,t	   delimiters   	t   headerN(   t   joint   mapt   strR   R	   R
   R   R   R   t   savetxtR   (   R   t   filenamet   head(    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt   save<   s    6c         C   s‘   t  |  d ƒ } | j ƒ  } | j ƒ  | j d ƒ j d ƒ j d ƒ } t j |  d d ƒ} t | d | d | d | d	 ƒ } | j	 | ƒ | S(
   Nt   rs   
t   #R   t   skiprowsi   i    i   i   (
   t   opent   readlinet   closet   rstript   lstript   splitR   t   loadtxtR   R   (   R&   t   fR!   t   elementsR   R   (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyR,   @   s    
!%c         C   s	  t  j |  j |  j |  j |  j d d f ƒ } |  j d } x_ t |  j |  j ƒ D]H } d | | |  j | | d d f <d | | |  j | | d f <qT Wt j |  j | d d ƒd } t |  j	 |  j
 | j d d |  j | j d d ƒ } | j | ƒ | S(   s?   Collape matrix into insertions.  Will reduce span on chromosomei   i   t   modet   validi    (   R   R   R   R   R   R    t   correlate2dR   R   R   R	   R   R
   t   assign_track(   R   t   patternt   midt   it   inst   insertion_track(    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt   getInsJ   s    1##9c         C   s6  | d k r |  j } n  | d k r0 |  j } n  t j ƒ  } t j |  j d | d | ƒ d d d d d |  j |  j d | | d g d t	 j
 d	 ƒ ƒt j |  j ƒ t j d
 ƒ | rÉ t j | ƒ n  | r(| j | ƒ t j | ƒ d j | j d ƒ d  d g ƒ } t j | |  j d d ƒn
 | j ƒ  d S(   s   Plot 2d ReadMatR   R   t   origint   interpolationt   nearestt   extenti   t   cmapt   Greyss   Insert sizet   .iÿÿÿÿt   txtR    s   	N(   R   R   R   t   pltt   figuret   imshowR   R	   R
   t   cmt   get_cmapt   xlabelR   t   ylabelt   titlet   savefigR.   R"   R1   R   R%   R   t   show(   R   R&   RN   R   R   t   figt	   filename2(    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt   plotU   s$    0#N(   t   __name__t
   __module__t   __doc__R   R   t   FalseR   R   R(   t   staticmethodR,   R>   RS   (    (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyR   	   s   		"		
		t   FragmentMat2Dc           B   s,   e  Z d  Z e d „ Z d „  Z d „  Z RS(   s=   Class that stores fragment information in 2D matrix accordingc         C   s)   t  j |  | | | | | ƒ | |  _ d  S(   N(   R   R   t   atac(   R   R   R	   R
   R   R   RZ   (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyR   r   s    c         C   sQ  | j  |  j } |  j d k r“ | j  d d | j |  j } | d k rM| |  j k  rM| |  j k  rM| d k rM|  j | | f c d 7<qMnº | j } | j d } | d k rû | |  j k  rû | |  j k  rû | d k rû |  j | | f c d 7<n  | d k rM| |  j k  rM| |  j k  rM| d k rM|  j | | f c d 7<n  d  S(   Nt   centersi   i   i    (	   t   insertR   R5   t   leftR	   R   R   R   t   right(   R   t   fragmentt   rowt   colt   col1t   col2(    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt	   updateMatu   s    6	66c         C   s7   t  | |  j |  j |  j |  j |  j |  j ƒ |  _ d S(   s   Make 2D matrixN(   R   R   R	   R
   R   R   RZ   R   (   R   t   bamfile(    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyR   ‚   s    (   RT   RU   RV   t   TrueR   Rd   R   (    (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyRY   p   s   	t	   BiasMat2Dc           B   s)   e  Z d  Z d „  Z d „  Z d „  Z RS(   sM   Class that stores fragment probabilities in 2D matrix according to bias modelc         C   s8   t  j |  | | | | | ƒ t j |  j j ƒ |  _ d  S(   N(   R   R   R   t   onesR   R   (   R   R   R	   R
   R   R   (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyR   ‰   s    c         C   sl  |  j  d } | j |  j | |  j | ƒ } | j so t j | d k ƒ d } t j | t | | ƒ ƒ } n  t j |  j  |  j	 |  j  |  j  d d f ƒ } |  j  d } x_ t
 |  j	 |  j  ƒ D]H } d | | |  j	 | | d d f <d | | |  j	 | | d f <qÃ WxV t
 |  j  |  j	 ƒ D]> } t j t j | | | d d … f d d ƒƒ |  j | <q&Wd S(   s5   Make 2D matrix representing sequence bias preferencesi   i    i   NR5   R6   (   R   R   R	   R
   t   logR   t   wheret   minR   R   R   t   expt   convolveR   (   R   t
   bias_trackt   offsett   biast   nonzeroR9   R:   R;   (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt   makeBiasMatŒ   s     	 1##c         C   sZ   | j  |  j |  j ƒ } |  j t j t j | |  j j d ƒ |  j j d d ƒ|  _ d  S(   Ni   t   ordert   F(   R   R   R   R   R   t   reshapet   tileR   (   R   t   insertsizest   inserts(    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt   normByInsertDistš   s    (   RT   RU   RV   R   Rr   Ry   (    (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyRg   ‡   s   		(    (   t   numpyR   t   scipyR    t   matplotlib.pyplott   pyplotRG   t   matplotlib.cmRJ   t   pyatac.tracksR   t	   pyximportt   installt   get_includet	   fragmentsR   R   RY   Rg   (    (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/chunkmat2d.pyt   <module>   s    g