ó
?īec           @   sT   d  Z  d d l Z d d l m Z d d l m Z d d l Z d   Z d   Z	 d S(   s@   
Script to get read counts  distribution

@author: Alicia Schep
i’’’’N(   t	   ChunkList(   t   AlignmentFilec         C   s$   |  | k r |  | k  r t  St Sd  S(   N(   t   Truet   False(   t   xt   startt   end(    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_counts.pyt   _between   s    c   
      C   s×  |  j  d k rC d j t j j |  j  j d  d d ! |  _  n  t j	 |  j  } t
 j t |  d t
 j } t |  j  } d } x| D]} x | j | j t d | j |  j  | j |  j  D]É } | j rĖ | j rĖ |  j r| j d } t | j  d } n | j } t | j  } | | d }	 t | |  j |  j  rt | | j | j  s~t |	 | j | j  r| | c d 7<qqĖ qĖ W| d 7} q W| j   t
 j |  j  d | d	 d
 d d d S(   s$   function to get fragment sizes

    t   .i    i’’’’t   dtypei   i   i   s   .counts.txt.gzt	   delimiters   
t   fmts   %iN(    t   outt   Nonet   joint   ost   patht   basenamet   bedt   splitR    t   readt   npt   zerost   lent   intR   t   bamt   fetcht   chromt   maxR   t   upperR   t   is_proper_pairt
   is_reverset   atact   post   abst   template_lengthR   t   lowert   closet   savetxt(
   t   argst   chunkst   matt	   bamHandlet   jt   chunkR   t   l_post   ilent   r_pos(    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_counts.pyt
   get_counts   s(    4<		H
(
   t   __doc__R   t   pyatac.chunkR    t   pysamR   t   numpyR   R   R0   (    (    (    s7   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_counts.pyt   <module>   s   	