ó
?îec           @   s®   d  Z  d d l Z d d l Z d d l j Z d d l m Z d d l	 Z	 d d l
 Z
 d d l m Z d d l m Z d d l m Z d „  Z d d d	 „  ƒ  YZ d
 „  Z d S(   sv   
Function to make plot of aggregate signal around sites.

@author: Alicia Schep, Greenleaf lab at Stanford University
iÿÿÿÿN(   t   Pool(   t   BedGraphFile(   t	   ChunkList(   t   read_chrom_sizesc         C   s)  |  \ } } t  | j ƒ } t j | j | j d ƒ } | j rs d } t j t | ƒ | j | j d f ƒ } n t j | j | j d ƒ } xw| D]o} y!| j ƒ  | j d k rð | j d k rð | j	 d | j
 d | j d | j ƒ n  | j | j | j | j ƒ } | j d k rÍ| j d k rÍt | ƒ | j | j d k rÍ| j d k r”t j t j | j | j d t | ƒ ƒ | f ƒ } qÍt j | t j | j | j d t | ƒ ƒ f ƒ } n  | j d k rò| d d d … } n  | j rt j | ƒ } n  | j r)d | | d k  <n  | j r€| }	 d |	 t j |	 ƒ <| t j t | ƒ ƒ t j t | ƒ ƒ d k } n  | j r | | | <| d 7} n d | t j | ƒ <| | 7} Wq— t k
 r}
 d	 | j ƒ  d
 GHt j ƒ  d GH| j ƒ  |
 ‚ q— Xq— W| j ƒ  | j r!| S| Sd S(   s0   Get aggregate signal around a set of sites

    i   i    t	   chromDictt   upt   downt   -Niÿÿÿÿs"   Caught exception when processing:
s   
(    (   R   t   bgt   npt   zerosR   R   t   allt   lent   centert   slopt   chrst   readt   chromt   startt   endt   hstackt   strandt   expt   positivet   scalet   isnant   sumt   abst	   Exceptiont   asBedt	   tracebackt	   print_exct   close(   t   argt   chunkst   paramsR   t   aggt   countert   matt   chunkt   sigt   tmpt   e(    (    s@   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/signal_around_sites.pyt   _signalHelper   sV    	,
(>*9			5	



	t   _signalParamsc           B   s   e  Z d  „  Z RS(   c	   	      C   sR   | |  _  | |  _ | |  _ t | ƒ |  _ | |  _ | |  _ | |  _ | |  _ d  S(   N(	   R   R   R   R   R   R   R   R   R   (	   t   selft   bedgrapht   sizesR   R   R   R   R   R   (    (    s@   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/signal_around_sites.pyt   __init__N   s    						(   t   __name__t
   __module__R0   (    (    (    s@   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/signal_around_sites.pyR,   M   s   c   	   	   C   s)  |  j  s= d j t j j |  j ƒ j d ƒ d d !ƒ |  _  n  t j |  j d |  j	 ƒ} t
 |  j |  j |  j |  j |  j |  j |  j |  j ƒ } | j d t |  j d t | ƒ ƒ ƒ } t d |  j ƒ } | j t t | t j | ƒ ƒ ƒ } | j ƒ  | j ƒ  |  j rit j | ƒ } t j |  j  d | d	 d
 d d ƒd | t j  | ƒ <t j! | d d ƒ} n t! | ƒ } |  j" s%|  j# rš| t | ƒ } n  t$ j% ƒ  } t$ j& t' |  j |  j d ƒ | ƒ t$ j( d ƒ t$ j) d ƒ | j* |  j  d ƒ t$ j | ƒ t j |  j  d | d	 d ƒn  d S(   s;   function to get signal from a track around some sites

    t   .i    iÿÿÿÿt
   strand_colt   itemsi   t	   processess   .tracks.txt.gzt	   delimitert   ,t   fmts   %1.5gt   axisi   s   Position relative to Sites   Signal Intensitys   .agg.track.epss   .agg.track.txts   	N(+   t   outt   joint   ost   patht   basenamet   bedt   splitR   R   R   R,   R   R/   R   R   R   R   R   R   t   mint   coresR   R    t   mapR+   t   zipt	   itertoolst   repeatR    R	   t   vstackt   savetxtR   R   t   no_aggt   normt   pltt   figuret   plott   ranget   xlabelt   ylabelt   savefig(	   t   argsR"   R#   t   setst   poolR)   R&   t   resultt   fig(    (    s@   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/signal_around_sites.pyt
   get_signalX   s4    	4!($

	#		$(    (   t   __doc__R=   t   numpyR	   t   matplotlib.pyplott   pyplotRL   t   multiprocessingR    RF   R   t   pyatac.bedgraphR   t   pyatac.chunkR   t   pyatac.utilsR   R+   R,   RX   (    (    (    s@   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/signal_around_sites.pyt   <module>   s   	5