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

@author: Alicia Schep, Greenleaf lab at Stanford University
iÿÿÿÿN(   t   Pool(   t	   ChunkList(   t   PWMt
   setup_argst   include_dirs(   t   InsertionTrack(   t   read_chrom_sizes_from_fastac      	   C   s‡  |  \ } } y3d } t  j t | j ƒ | j | j d f ƒ } xú | D]ò } t | j | j | j	 ƒ } | j
 rÎ | j | j d | j d | j d | j ƒ| | j | j | j d | j d | j ƒ7} nY | j | j d | j d | j d | j ƒ| | j | j | j d | j d | j ƒ7} | t | j ƒ 7} qH WWn; t k
 r|} d | j ƒ  d	 GHt j ƒ  d
 GH| ‚ n X| | f S(   sN   "Helper function for multiprocessing acquisition of sequence around insertionsg        i   t   lowert   uppert   atact   upt   downs"   Caught exception when processing:
s   
(    (   t   npt   zerost   lent   nucleotidesR
   R   R   t   chromt   startt   endt   symt   calculateInsertionst   bamR   R   R	   t   getInsertionSequencest   fastat   calculateStrandedInsertionst   getStrandedInsertionSequencest   sumt   valst	   Exceptiont   asBedt	   tracebackt	   print_exc(   t   argt   chunkst   paramst   nt   matt   chunkt   inst   e(    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_pwm.pyt
   _pwmHelper   s$    ,	+1+.

t   _PWMParametersc           B   s#   e  Z d  Z d d e e d „ Z RS(   s0   Class to store parameters related to getting pwmi    iÐ  c	   	      C   sa   | |  _  | |  _ | |  _ | |  _ | |  _ | |  _ | |  _ d d d d g |  _ | |  _ d  S(   Nt   At   Ct   Gt   T(	   R   R
   R   R   R   R   R	   R   R   (	   t   selfR   R
   R   R   R   R   R	   R   (    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_pwm.pyt   __init__.   s    							(   t   __name__t
   __module__t   __doc__t   TrueR/   (    (    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_pwm.pyR)   ,   s   iPÃ  iè  c         C   s  |  j  s= d j t j j |  j ƒ j d ƒ d d !ƒ |  _  n  t |  j ƒ } |  j	 d k r’ t j | d | d |  j ƒ} | j d | | ƒ } n3 t j |  j	 d | d |  j ƒ} | j d	 | ƒ } t d
 |  j d |  j d |  j d |  j d |  j d |  j d |  j d |  j ƒ } t d |  j ƒ } | j t t | t j | ƒ ƒ ƒ } | j ƒ  | j ƒ  d }	 t j t | j ƒ | j  | j! d f ƒ }
 x* | D]" } |
 | d 7}
 |	 | d 7}	 q™W|
 |	 :}
 |  j	 rðt" j# | |  j | j ƒ } n t" j$ |  j | j ƒ } |
 t j% t j | |
 j& d ƒ |
 j& ƒ }
 |  j rè|
 d d … d |  j d … f } |
 d d … |  j d … f } t j' t j( | ƒ ƒ } | | d } t j) | t j' t j( | d d … d |  j … f ƒ ƒ f ƒ }
 n  t* |
 |  j |  j | j ƒ } | j+ |  j  d ƒ d S(   s*   Functiono obtain PWM around ATAC insertiont   .i    iÿÿÿÿt	   splitsizet   offsett   itemst	   chromDictt
   min_offsett   basesR   R
   R   R   R   R   R	   R   t	   processesg        i   Ni   s   .PWM.txt(,   t   outt   joint   ost   patht   basenameR   t   splitR   R   t   bedt   NoneR   t   convertChromSizest   flankt   readR)   R   R   R	   R   R    t   corest   mapR(   t   zipt	   itertoolst   repeatt   closeR   R   R   R   R
   R   t   seqt   getNucFreqsFromChunkListt   getNucFreqst   reshapet   shapet   fliplrt   flipudt   hstackR   t   save(   t   argsR:   R5   t   chrsR!   t   setsR"   t   poolt   tmpR#   t   resultt   it	   normfreqst   leftt   rightt   rightflippedt   combinedt   pwm(    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_pwm.pyt   get_pwm:   s@    	4!*'$

,
	,	#C(    (   R2   R>   t   numpyR   RJ   t   multiprocessingR    R   t
   pyatac.seqRM   t   pyatac.chunkR   t   pyatac.biasR   t	   pyximportt   installt   get_includet   pyatac.tracksR   t   pyatac.utilsR   R(   R)   Rc   (    (    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_pwm.pyt   <module>   s   	