ó
?îec           @   sh   d  Z  d d l Z d d l Z e j d i e j ƒ  d 6ƒ d d l m Z m Z d d d „  ƒ  YZ	 d S(	   sk   
Classes for working with fragment distribution

@author: Alicia Schep, Greenleaf Lab, Stanford University
iÿÿÿÿNt
   setup_argst   include_dirs(   t   getAllFragmentSizest   getFragmentSizesFromChunkListt   FragmentSizesc           B   sS   e  Z d  Z e d d „ Z d d „ Z d d d d „ Z d „  Z e	 d „  ƒ Z
 RS(   s,   Class for storing fragment size distributionc         C   s(   | |  _  | |  _ | |  _ | |  _ d  S(   N(   t   lowert   uppert   valst   atac(   t   selfR   R   R   R   (    (    s:   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/fragmentsizes.pyt   __init__   s    			c         C   s   | d  k r0 t | |  j |  j d |  j ƒ} n$ t | | |  j |  j d |  j ƒ} | t j | ƒ t j | ƒ d k |  _ d  S(   NR   i    (	   t   NoneR   R   R   R   R   t   npt   sumR   (   R	   t   bamfilet   chunkst   sizes(    (    s:   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/fragmentsizes.pyt   calculateSizes   s    $$c         C   s«   | r5 y |  j  | |  j SWq§ t d ƒ ‚ q§ Xnr | d  k rM |  j } n  | d  k re |  j } n  | |  j } | |  j } y |  j  | | !SWn t d ƒ ‚ n Xd  S(   Ns+   Looks like size doesn't match FragmentSizess@   Looks like dimensions from get probaby don't match FragmentSizes(   R   R   t	   ExceptionR   R   (   R	   R   R   t   sizet   y1t   y2(    (    s:   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/fragmentsizes.pyt   get   s    c         C   s¡   t  | d ƒ } | j d ƒ | j t |  j ƒ d ƒ | j d ƒ | j t |  j ƒ d ƒ | j d ƒ | j d j t t |  j ƒ  ƒ ƒ d ƒ | j ƒ  d S(   s&   Save Fragment Distribution informationt   ws   #lower
s   
s   #upper
s   #sizes
s   	N(	   t   opent   writet   strR   R   t   joint   mapR   t   close(   R	   t   filenamet   f(    (    s:   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/fragmentsizes.pyt   save-   s    )c         C   sB  t  |  d ƒ } d } xã | D]Û } d | k r7 d } q d | k rL d } q d | k ra d } q d	 | k rv d
 } q | d k rš t | j d ƒ ƒ } q | d k r¾ t | j d ƒ ƒ } q | d k r t j t t | j d ƒ j d ƒ ƒ ƒ } q q Wy t	 | | d | ƒ} Wn t
 k
 r3t d ƒ ‚ n X| j ƒ  | S(   s<   Create FragmentDistribution object from text descriptor filet   rt    s   #lowerR   s   #upperR   s   #sizesR   t   #t   others   
s   	R   sN   FragmentDistribution decriptor file appeas to be missing someneeded components(   R   t   intt   stripR   t   arrayR   t   floatt   rstript   splitR   t	   NameErrorR   R   (   R   t   infilet   statet   lineR   R   t   fragmentsizest   new(    (    s:   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/fragmentsizes.pyR   7   s0    				1
N(   t   __name__t
   __module__t   __doc__t   TrueR   R
   R   R   R    t   staticmethodR   (    (    (    s:   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/fragmentsizes.pyR      s   	
(    (
   R3   t   numpyR   t	   pyximportt   installt   get_includet   pyatac.fragmentsR   R   R   (    (    (    s:   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/fragmentsizes.pyt   <module>   s
   