ó
?îec           @   s¢   d  Z  d d l m Z d d l Z d d l Z d d l j Z d d l j	 Z	 d d l
 m Z d d l m Z d „  Z d d d „  ƒ  YZ d	 e f d
 „  ƒ  YZ d S(   sw   
General tools for dealing with ATAC-Seq data using Python.

@author: Alicia Schep, Greenleaf Lab, Stanford University
iÿÿÿÿ(   t   resource_filenameN(   t   Track(   t   smoothc         C   s1   t  d |  d ƒ } t j j | ƒ r) | S|  Sd  S(   Ns
   pyatac.pwms   .PWM.txt(   R    t   ost   patht   isfile(   t   namet   out(    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyt	   pwm_parse   s    t   PWMc           B   s/   e  Z d  Z d „  Z d „  Z e d „  ƒ Z RS(   s$   Class for storing Tn5 preference pwmc         C   s(   | |  _  | |  _ | |  _ | |  _ d  S(   N(   t   matt   upt   downt   nucleotides(   t   selfR
   R   R   R   (    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyt   __init__   s    			c         C   só   t  | d ƒ } | j d ƒ | j 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 |  j ƒ d ƒ | j d	 ƒ x4 |  j D]) } | j d j t t | ƒ ƒ d ƒ q¸ W| j	 ƒ  d
 S(   s6   write text output description of PWM object attributest   ws   #PWM Descriptor File
s(   #Contains PWM and pertinent information
s   #up
s   
s   #down
s   #nucleotides
s   	s   #mat
N(
   t   opent   writet   strR   R   t   joinR   R
   t   mapt   close(   R   t   filenameR   t   row(    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyt   save   s    'c   
      C   s  t  |  ƒ } t | d ƒ } d } g  } x| D]ý } d | k rI d } q. d | k r^ d } q. d | k rs d } q. d	 | k rˆ d
 } q. | d k r¬ t | j d ƒ ƒ } q. | d k rÐ t | j d ƒ ƒ } q. | d
 k rô | j d ƒ j ƒ  } q. | d k r. | j t t | j d ƒ j d ƒ ƒ ƒ q. q. W| j ƒ  y" t	 t
 j | ƒ | | | ƒ }	 Wn t k
 rzt d ƒ ‚ n X|	 S(   s+   Create PWM object from text descriptor filet   rt    s   #upR   s   #downR   s   #matR
   s   #nucleotidesR   s   
s   	s=   PWM decriptor file appeas to be missing someneeded components(   R   R   t   intt   stript   splitt   appendR   t   floatR   R	   t   npt   arrayt	   NameErrort	   Exception(
   R   R   t   infilet   stateR
   t   lineR   R   R   t   new(    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyR   .   s8    				/
"(   t   __name__t
   __module__t   __doc__R   R   t   staticmethodR   (    (    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyR	      s   		t   InsertionBiasTrackc           B   sG   e  Z d  Z e d „ Z d „  Z d d d d d „ Z d d d „ Z RS(   s,   Class for getting and storing insertion biasc      	   C   s&   t  j |  | | | d d d | ƒd  S(   NR   s   insertion biast   log(   R   R   (   R   t   chromt   startt   endR.   (    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyR   S   s    c         C   s™   |  j  | d | j d | j ƒt j |  | ƒ } t j | | j ƒ } t j | t	 j
 | j ƒ d d ƒd |  _ |  j | j 7_ |  j | j 8_ d S(   s,   compute bias track based on sequence and pwmR   R   t   modet   validi    N(   t   slopR   R   t   seqt   get_sequencet
   seq_to_matR   t   signalt	   correlateR!   R.   R
   t   valsR0   R1   (   R   t   fastat	   chromDictt   pwmt   sequencet   seqmat(    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyt   computeBiasU   s    +c         C   si   t  j |  | | | ƒ } | d k r( | S| rK |  j r; | St j | ƒ Sn |  j ra t j | ƒ S| Sd S(   s#   Obtain values for particular regionN(   R   t   gett   NoneR.   R!   t   exp(   R   R0   R1   t   posR.   R   (    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyRA   ]   s    		i7   t   flatc         C   sÄ   |  j  r t j |  j ƒ } n	 |  j } t | | | d t ƒ} | d } |  j  r t j  | | | !| | | | !ƒ |  _ n! | | | !| | | | !|  _ |  j | |  _ |  j | |  _ d S(   s1   Make bias a reflection of score in a given windowt   normi   N(   R.   R!   RC   R:   R   t   FalseR0   R1   (   R   t	   windowlent   windowt   ebiast   smoothedt   flank(    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyt   getLocalbiasl   s    		
	-!N(	   R)   R*   R+   t   TrueR   R@   RB   RA   RM   (    (    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyR-   Q   s
   	(    (   R+   t   pkg_resourcesR    R   t   numpyR!   t   scipy.signalR8   t
   pyatac.seqR5   t   pyatac.tracksR   t   pyatac.utilsR   R   R	   R-   (    (    (    s1   /tmp/pip-install-bGcd2k/NucleoATAC/pyatac/bias.pyt   <module>   s   	9