ó
?îec           @   sÂ   d  Z  d d l Z d d l 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 m Z m Z d d l m Z m Z d „  Z d „  Z d d d	 „  ƒ  YZ d
 d d „ Z d S(   s3   
Script to compute Tn5 bias

@author: Alicia Schep
iÿÿÿÿN(   t	   ChunkList(   t   InsertionBiasTrackt   PWM(   t   read_chrom_sizes_from_fastat   shell_commandc         C   s‰   |  \ } } y; t  | j | j | j ƒ } | j | j | j | j ƒ Wn; t k
 r„ } d | j	 ƒ  d GHt
 j ƒ  d GH| ‚ n X| S(   s:   Helper function to multiprocess computation of bias trackss"   Caught exception when processing:
s   
(    (   R   t   chromt   startt   endt   computeBiast   fastat   chrst   pwmt	   Exceptiont   asBedt	   tracebackt	   print_exc(   t   argt   chunkt   paramst   biast   e(    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_track.pyt   _biasHelper   s     

c         C   s‰   t  | d d ƒ } y8 x1 t |  j d ƒ D] } | j | ƒ |  j ƒ  q) WWn- t k
 rz } d GHt j ƒ  d GH| ‚ n X| j ƒ  t	 S(   s)   Function to handle writing of bias outputs   .Scores.bedgrapht   at   STOPs.   Caught exception when writing insertion track
(    (
   t   opent   itert   gett   write_trackt	   task_doneR   R   R   t   closet   True(   t   track_queuet   outt
   out_handlet   trackR   (    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_track.pyt
   _writeBias    s    


t   _BiasParamsc           B   s   e  Z d  Z d „  Z RS(   s1   Class to store parameter for _biasHelper functionc         C   s.   t  | ƒ |  _ | |  _ t j | ƒ |  _ d  S(   N(   R   R
   R	   R   R   R   (   t   selfR	   R   (    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_track.pyt   __init__1   s    	(   t   __name__t
   __module__t   __doc__R&   (    (    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_track.pyR$   /   s   i ¡ iè  c         C   s¸  |  j  d k r† |  j d k	 rR d j t j j |  j ƒ j d ƒ d d !ƒ |  _  q† d j t j j |  j ƒ j d ƒ d d !ƒ |  _  n  t	 |  j |  j
 ƒ } |  j d k rÛ t j | j d | ƒ} | j d | | ƒ } nD t j |  j ƒ } | j | j j ƒ  ƒ | j ƒ  | j d | ƒ } t d t d | t j g  | D] } | j ƒ  ^ q<ƒ ƒ ƒ } t j d t d	 |  j d	 ƒ ƒ } t |  j  d
 d ƒ }	 |	 j ƒ  t j d | ƒ }
 t j d t d |
 |  j  f ƒ } | j ƒ  xP | D]H } | j  t! t" | t# j$ | ƒ ƒ ƒ } x | D] } |
 j% | ƒ qWqäW| j ƒ  | j ƒ  |
 j% d ƒ | j ƒ  t& j' |  j  d
 |  j  d d t( ƒt) d |  j  d
 ƒ t& j* |  j  d d d d t( ƒd S(   s$   function to compute bias track

    t   .i    iÿÿÿÿt	   splitsizet   itemst   basesi   t	   processesi   s   .Scores.bedgrapht   wt   maxsizet   targett   argsR   s   .Scores.bedgraph.gzt   forces   rm t   presett   bedN(+   R    t   NoneR5   t   joint   ost   patht   basenamet   splitR	   R$   R   R    t   convertChromSizesR
   t   readt   checkChromst   keyst   merget   maxt   intt   npt   meant   lengtht   mpt   Poolt   coresR   R   t   JoinableQueuet   ProcessR#   R   t   mapR   t   zipt	   itertoolst   repeatt   putt   pysamt   tabix_compressR   R   t   tabix_index(   R2   R-   R+   R   t   chunkst   setsR   t   maxQueueSizet   poolR!   t   write_queuet   write_processt   jt   tmpR"   (    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_track.pyt   make_bias_track6   s<    44
?"
!
$


$(    (   R)   R8   t   multiprocessingRF   RM   R   RP   t   numpyRC   t   pyatac.chunkR    t   pyatac.biasR   R   t   pyatac.utilsR   R   R   R#   R$   R[   (    (    (    s<   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/make_bias_track.pyt   <module>   s   		