ó
?îec           @   sÏ   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
 ƒ  d d l m Z d d l m Z d d l m Z m Z d d l m Z d „  Z d „  Z d	 d
 d „ Z d S(   s6   
Script to make coverage track

@author: Alicia Schep
iÿÿÿÿN(   t   CoverageTrack(   t	   ChunkList(   t   shell_commandt   read_chrom_sizes_from_bam(   t   FragmentMat2Dc         C   s  |  \ } } y¸ | j  d } t | j | j | | j | | j | j | j ƒ } | j | j	 ƒ t
 | j | j | j ƒ } | j | d | j d | j d | j  ƒ| j | j t | j  ƒ 9_ Wn; t k
 r} d | j ƒ  d GHt j ƒ  d GH| ‚ n X| S(   s;   Computes coverage track for a particular set of bed regionsi   t   lowert   uppert
   window_lens"   Caught exception when processing:
s   
(    (   t   windowR   t   chromt   startt   endR   R   t   atact   makeFragmentMatt   bamR    t   calculateCoveraget   valst   scalet   floatt	   Exceptiont   asBedt	   tracebackt	   print_exc(   t   argt   chunkt   argst   offsett   matt   covt   e(    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_cov.pyt
   _covHelper   s    5(#

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   .cov.bedgrapht   at   STOPs-   Caught exception when writing coverage 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_cov.pyt	   _writeCov'   s    


iPÃ  iè  c         C   s“  |  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  xP | D]H } | j t t | t j  |  ƒ ƒ ƒ } x | D] } |
 j! | ƒ qð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 coverages

    t   .i    iÿÿÿÿt	   splitsizet   itemst   basesi   t	   processesi   s   .cov.bedgrapht   wt   maxsizet   targetR   R    s   .cov.bedgraph.gzt   forces   rm t   presett   bedN('   R)   R7   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
   t   mapR   t   zipt	   itertoolst   repeatt   putt   pysamt   tabix_compressR'   R   t   tabix_index(   R   R0   R.   t   chrst   chunkst   setsR   t   maxQueueSizet   pool1R*   t   write_queuet   write_processt   jt   tmpR+   (    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_cov.pyt   get_cov5   s:    	44
?"
!
$


$(   t   __doc__R:   t   multiprocessingRF   RM   t   numpyRC   RP   R   t	   pyximportt   installt   pyatac.tracksR    t   pyatac.chunkR   t   pyatac.utilsR   R   t   pyatac.chunkmat2dR   R   R,   R\   (    (    (    s4   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_cov.pyt   <module>   s    
		