ó
?îec           @   sN   d  Z  d d l Z d d l j Z d d l m Z d d l m Z d   Z	 d S(   sA   
Script to get fragment size distribution

@author: Alicia Schep
iĸĸĸĸN(   t   FragmentSizes(   t	   ChunkListc         C   sW  |  j  d k rC d j t j j |  j  j d  d d ! |  _  n  t d |  j	 d |  j
 d |  j  } |  j rĒ t j |  j  } | j   | j |  j |  n | j |  j  | j |  j  d  |  j sSt j   } t j t | j	 | j
  | j | j	 | j
  d |  j  t j d	  t j d
  | j |  j  d  t j |  n  d S(   s$   function to get fragment sizes

    t   .i    iĸĸĸĸt   lowert   uppert   atacs   .fragmentsizes.txtt   labels   Fragment Sizet	   Frequencys   .fragmentsizes.epsN(   t   outt   Nonet   joint   ost   patht   basenamet   bamt   splitR    R   R   R   t   bedR   t   readt   merget   calculateSizest   savet   no_plott   pltt   figuret   plott   ranget   gett   xlabelt   ylabelt   savefigt   close(   t   argst   sizest   chunkst   fig(    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_sizes.pyt	   get_sizes   s     4$	
	:(
   t   __doc__R   t   matplotlib.pyplott   pyplotR   t   pyatac.fragmentsizesR    t   pyatac.chunkR   R#   (    (    (    s6   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/get_sizes.pyt   <module>   s
   