ó
?îec           @   s   d  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 j	 Z	 d d l
 m Z d d l j Z d „  Z d d	 d „  ƒ  YZ d „  Z d S(
   si   
Gets aggregate nuc frequency around sites.

@author: Alicia Schep, Greenleaf lab at Stanford University
iÿÿÿÿN(   t   Pool(   t	   ChunkListc   	   	   C   s  |  \ } } t  j | j ƒ } d } y³ x¬ | D]¤ } | j ƒ  | j d | j d | j d | j | j ƒ t	 j
 | | j ƒ } t	 j | | j ƒ } t | ƒ | j | j d | j k r. | | 7} | d 7} q. q. WWn; t k
 r} d | j ƒ  d GHt j ƒ  d GH| ‚ n X| | f S(	   sP   Helper function for multiprocessing acquisition of sequence content around sitesg        t	   chromDictt   upt   downi   s"   Caught exception when processing:
s   
(    (   t   npt   zerost   matsizet   centert   slopt   chrsR   R   t   dinucleotidet   seqt   get_sequencet   fastat
   seq_to_matt   nucleotidest   lent	   Exceptiont   asBedt	   tracebackt	   print_exc(	   t   argt   chunkst   paramst   matt   nt   chunkt   sequencet   submatt   e(    (    s;   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_nucleotide.pyt   _nucleotideHelper   s$    
,'


t   _NucleotideParametersc           B   s   e  Z d  Z e d „ Z RS(   s8   Class to store parameters related to getting nucleotidesc         C   sÉ   | |  _  | |  _ | |  _ t j | ƒ |  _ | r d } g  } x3 t j | d d ƒD] } | j d j	 | ƒ ƒ qU W| |  _
 n d d d d g |  _
 t |  j
 ƒ |  j  |  j d	 f |  _ | |  _ d  S(
   Nt   CGATt   repeati   t    t   At   Ct   Gt   Ti   (   R   R   R   t   utilst   read_chrom_sizes_from_fastaR
   t	   itertoolst   productt   appendt   joinR   R   R   R   (   t   selfR   R   R   R   t   nucst   dinucst   p(    (    s;   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_nucleotide.pyt   __init__+   s    			&(   t   __name__t
   __module__t   __doc__t   FalseR2   (    (    (    s;   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_nucleotide.pyR    )   s   c         C   sØ  |  j  s= d j t j j |  j ƒ j d ƒ d d !ƒ |  _  n  t j |  j d |  j	 ƒ} t
 |  j |  j |  j |  j ƒ } | j d d ƒ } t d |  j ƒ } | j t t | t j | ƒ ƒ ƒ } | j ƒ  | j ƒ  t j | j ƒ } d } x* | D]" } | | d 7} | | d	 7} qô W| | } |  j rtt j | j | j ƒ }	 | t j t j |	 | j d	 ƒ | j ƒ } n  t j  t j! | j ƒ d
 d
 … t j" f | j# d ƒ f ƒ }
 t j$ |  j  d |
 d d d d ƒd
 S(   s/   Function to obain sequence content around sitest   .i    iÿÿÿÿt
   strand_colt   basesi'  t	   processesg        i   Ns   |S8s   .nucfreq.txtt	   delimiters   	t   fmts   %s(%   t   outR-   t   ost   patht   basenamet   bedt   splitR   t   readt   strandR    R   R   R   R   R    t   corest   mapR   t   zipR*   R"   t   closeR   R   R   t   normR   t   getNucFreqsR   t   reshapet   shapet   hstackt   arrayt   newaxist   astypet   savetxt(   t   argsR   R   t   setst   poolt   tmpt   resultR   t   it	   normfreqsR=   (    (    s;   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_nucleotide.pyt   get_nucleotide=   s(    	4!$


	/=(    (   R5   R>   t   numpyR   R*   R   t   multiprocessingR    t
   pyatac.seqR   t   pyatac.chunkR   t   pyatac.utilsR(   R   R    RY   (    (    (    s;   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_nucleotide.pyt   <module>   s   	