ó
?îec           @   sÛ   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	 Z	 e	 j
 d i e j ƒ  d 6ƒ d d l m Z d d l m Z d d l m Z m Z d „  Z d	 „  Z d
 „  Z d d d „ Z d S(   s7   
Script to make insertion track

@author: Alicia Schep
iÿÿÿÿNt
   setup_argst   include_dirs(   t   InsertionTrack(   t	   ChunkList(   t   shell_commandt   read_chrom_sizes_from_bamc         C   sÉ   |  \ } } y{ | j  d } t | j | j | | j | ƒ } | j | j d | j d | j d | j	 ƒ| j
 | j  d d d d ƒWn; t k
 rÄ } d	 | j ƒ  d
 GHt j ƒ  d GH| ‚ n X| S(   sE   Computes smoothed insertion track for a particular set of bed regionsi   t   lowert   uppert   atact   windowt   gaussiant   modet   valids"   Caught exception when processing:
s   
(    (   t   smoothR   t   chromt   startt   endt   calculateInsertionst   bamR   R   R   t   smooth_trackt	   Exceptiont   asBedt	   tracebackt	   print_exc(   t   argt   chunkt   argst   offsett   inst   e(    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_ins.pyt   _insHelperSmooth   s    #+ 

c         C   s˜   |  \ } } yJ t  | j | j | j ƒ } | j | j d | j d | j d | j ƒWn; t	 k
 r“ } d | j
 ƒ  d GHt j ƒ  d GH| ‚ n X| S(   NR   R   R   s"   Caught exception when processing:
s   
(    (   R   R   R   R   R   R   R   R   R   R   R   R   R   (   R   R   R   R   R   (    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_ins.pyt
   _insHelper$   s    /

c         C   s‰   t  | d d ƒ } y8 x1 t |  j d ƒ D] } | j | ƒ |  j ƒ  q) WWn- t k
 rz } d GHt j ƒ  d GH| ‚ n X| j ƒ  t	 S(   Ns   .ins.bedgrapht   at   STOPs.   Caught exception when writing insertion track
(    (
   t   opent   itert   gett   write_trackt	   task_doneR   R   R   t   closet   True(   t   track_queuet   outt
   out_handlet   trackR   (    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_ins.pyt	   _writeIns0   s    


iPÃ  iè  c         C   sÃ  |  j  s€ |  j d k rL d j t j j |  j ƒ j d ƒ d d !ƒ |  _  q€ d j t j j |  j ƒ j d ƒ d d !ƒ |  _  n  |  j d k rÌ t	 |  j ƒ } t
 j | d | ƒ} | j d | | ƒ } n. t
 j |  j ƒ } | j ƒ  | j d | ƒ } t d t d | t j g  | D] } | j ƒ  ^ qƒ ƒ ƒ } t j d t d	 |  j d	 ƒ ƒ } t |  j  d
 d ƒ }	 |	 j ƒ  t j d | ƒ }
 t j d t d |
 |  j  f ƒ } | j ƒ  x€ | D]x } |  j rõ| j t t | t  j! |  ƒ ƒ ƒ } n$ | j t" t | t  j! |  ƒ ƒ ƒ } x | D] } |
 j# | ƒ q Wq¿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 get insertions

    t   .i    iÿÿÿÿt	   splitsizet   itemst   basesi   t	   processesi   s   .ins.bedgrapht   wt   maxsizet   targetR   R!   s   .ins.bedgraph.gzt   forces   rm t   presett   bedN()   R*   R8   t   Nonet   joint   ost   patht   basenameR   t   splitR   R   t   convertChromSizest   readt   merget   maxt   intt   npt   meant   lengtht   mpt   Poolt   coresR"   R'   t   JoinableQueuet   ProcessR-   R   R   t   mapR   t   zipt	   itertoolst   repeatR   t   putt   pysamt   tabix_compressR(   R   t   tabix_index(   R   R1   R/   t   chrst   chunkst   setsR   t   maxQueueSizet   pool1R+   t   write_queuet   write_processt   jt   tmpR,   (    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_ins.pyt   get_ins>   s>    	44
?"
!
	'$


$(   t   __doc__R;   t   multiprocessingRG   RN   t   numpyRD   RQ   R   t	   pyximportt   installt   get_includet   pyatac.tracksR   t   pyatac.chunkR   t   pyatac.utilsR   R   R   R   R-   R]   (    (    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_ins.pyt   <module>   s    			