ó
?îec           @   s2   d  Z  d d l j Z d d l m Z d   Z d S(   sŤ   
Takes as input a raw vplot and processes it for use in nucleosome calling
Use insert distribution at nuclesomal regions in peaks for normalization

@author: Alicia Schep
i˙˙˙˙N(   t   FragmentSizesc         C   s&  t  j j |  j  } | j |  j |  j |  j  | j   |  j	 d	 k	 rl t j |  j	  } | j |  n  |  j d k r | j d |  j  n  | j   |  j r÷ | j   | j |  j d  | j   | j |  j d  | j |  j d  n  | j |  j d  | j d |  j d  d	 S(
   s   process vplot

    i    t   sds   .vplot.Autocorr.epss   .vplot.InsertionProfile.epss   .vplot.InsertSizes.epss   .VMatt   filenames	   .VMat.epsN(   t   Vt   VMatt   opent   vplott   trimt   lowert   uppert   flankt
   symmetrizet   sizest   NoneR    t   norm_yt   smootht   normt
   plot_extrat   autoCorrt	   plot_autot   outt
   converto1dt   plot_1dt   plot_insertsizet   savet   plot(   t   argst   vmatt   nuc_dist(    (    s=   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/run_vprocess.pyt   run_vprocess   s"    

	

(   t   __doc__t   pyatac.VMatR   R   t   pyatac.fragmentsizesR    R   (    (    (    s=   /tmp/pip-install-bGcd2k/NucleoATAC/nucleoatac/run_vprocess.pyt   <module>   s   