ó
?îec           @   sŐ   d  Z  d d l Z d d l Z d d l m Z d d l Z d d l Z d d l m	 Z	 d d l
 m Z m Z d d l m Z d d l m Z d d l m Z d d	 l m Z d
   Z d d d     YZ d   Z d S(   s.   
Script to make V-plot

@author: Alicia Schep
i˙˙˙˙N(   t   Pool(   t   read_chrom_sizes_from_fasta(   t   InsertionBiasTrackt   PWM(   t	   BiasMat2D(   t	   ChunkList(   t   VMat(   t   FragmentSizesc   	   	   C   sŕ  |  \ } } t  j | j | j d | j d f  } xŁ| D]} yW| j   t | j | j | j d | j d | j	 | j | j d d  } | j
 d k	 rż | j | j
 d d n | j | j | j | j  t | j | j | j d | j	 | j | j | j  } | j |  | j | j  | j d | j | j d | j	 | j d | j d k  } | j r| | t  j |  7} n
 | | 7} Wq= t k
 r×} d	 | j   d
 GHt j   d GH|  q= Xq= W| S(   s@   function to make vplot for a particular set of bed regions

    i   i   t   emptyi    t   startt   endt   flipt   -s"   Caught exception when processing:
s   
N(    (   t   npt   zerost   uppert   lowert   flankt   centerR   t   chromR	   R
   t   bgt   Nonet
   read_trackt   computeBiast   fastat   chrst   pwmR   t   makeBiasMatt   normByInsertDistt   fragmentsizest   gett   strandt   scalet   sumt	   Exceptiont   asBedt	   tracebackt	   print_exc(	   t   argt   chunkst   paramst   matt   chunkt	   biastrackt   biasmatt   addt   e(    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_vplot.pyt   _biasVplotHelper   s2    *
%"')	
t   _BiasVplotParamsc           B   s   e  Z d    Z RS(   c	   	      C   s   | |  _  | |  _ | |  _ | |  _ | |  _ | |  _ |  j d  k ri t j |  |  _	 t
 |  |  _ n  t j |  |  _ d  S(   N(   R   R   R   R    R   R   R   R   t   openR   R   R   R   R   (	   t   selfR   R   R   R   R   R   t   sizesR    (    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_vplot.pyt   __init__:   s    						(   t   __name__t
   __module__R4   (    (    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_vplot.pyR0   9   s   c         C   s˛  |  j  s= d j t j j |  j  j d  d d ! |  _  n  t j |  j d |  j	 } | j d t
 |  j d t |    } t d |  j d |  j d	 |  j d
 |  j d |  j d |  j d |  j d |  j  } t d |  j  } | j t t | t j |    } | j   | j   t |  } t | |  j |  j  } | j d |  j  d  |  j  r| j!   | j" d |  j  d  | j# d |  j  d  n  | j$ |  j  d  d S(   s   function to make vplot

    t   .i    i˙˙˙˙t
   strand_colt   itemsi   R   R   R   R   R3   R    R   R   t	   processest   filenames   .Bias.Vplot.epss   .InsertionProfile.epss   .InsertSizes.epss
   .Bias.VMatN(%   t   outt   joint   ost   patht   basenamet   bedt   splitR   t   readR   t   mint   corest   lenR0   R   R   R   R   R3   R    R   R   R    t   mapR/   t   zipt	   itertoolst   repeatt   closeR!   R   t   plott
   plot_extrat
   converto1dt   plot_1dt   plot_insertsizet   save(   t   argsR'   t   setsR(   t   poolt   tmpt   resultt   vmat(    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_vplot.pyt   make_bias_vplotG   s&    	4(*$

	
(    (   t   __doc__t   numpyR   R>   t   multiprocessingR    R$   RI   t   pyatac.utilsR   t   pyatac.biasR   R   t   pyatac.chunkmat2dR   t   pyatac.chunkR   t   pyatac.VMatR   t   pyatac.fragmentsizesR   R/   R0   RX   (    (    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_vplot.pyt   <module>   s   	 