ó
&WMPc           @   sK   d  d l  Z  d  d l Z d  d l Z d  d l m Z d d d     YZ d S(   i’’’’N(   t   Get_Info_NUCMert   R1c           B   s,   e  Z d    Z d   Z d   Z d   Z RS(   c         C   sX   t  j d | d |  \ } } | GHt  j d | d | d |  \ } } | GHd  S(   Ns   python s   /CISA1/Filter1.py s   /CISA1/Extend.py t    (   t   commandst   getstatusoutput(   t   selft   infilet   CISA_St	   current_pt   st   o(    (    sG   /woldlab/castor/home/georgi/programs/CISA1.3/src/CISA1/Controllor_R1.pyt   Extend   s    !)c         C   s*   t  j d | d |  \ } } | GHd  S(   Ns   python s   /CISA1/Trim.py (   R   R   (   R   R   R   R	   R
   (    (    sG   /woldlab/castor/home/georgi/programs/CISA1.3/src/CISA1/Controllor_R1.pyt   Trim   s    !c         C   sī  t  | d  } t  |  } t   } xN t ru | j   j d d  } | sP Pn  | j   j d d  } | | | <q( Wd } x$ | j   D] } | t |  7} q Wx^ | D]V }	 |	 j d d  j   }
 x5 |
 D]- } | j d |  rĻ | j	 d |  qĻ qĻ WqŖ W| j
   | j
   d } x$ | j   D] } | t |  7} q+Wt  | d d  } | j d t |  d  | j d	 t |  d  | j d
 t |  t |  d d  d t |  GHd t |  GHt |  t |  GHd  S(   Ns   /CISA1/explained.txts   
t    i    t   >s   /infot   as   Total Base:s
   Rest Base:s   Ratio:%3.2fid   s   % 
s   Rest:s   Total:(   t   opent   dictt   Truet   readlinet   replacet   valuest   lent   splitt   gett   popt   closet   writet   strt   float(   R   R   R   t   ft   contigt   my_dictt   hR	   t   totalst   it   tmpt   jt   restst   fw(    (    sG   /woldlab/castor/home/georgi/programs/CISA1.3/src/CISA1/Controllor_R1.pyt   Get_explained_info   s:     		  
 
)c         C   s]   d GHt    } | j | | |  |  j | | |  |  j | |  |  j | |  d GHd  S(   Ns	   CISA1....s   CISA1 Done!(   R    t   StartR   R   R(   (   R   t   genome_lR   t   nucmerR   R   t   mywork(    (    sG   /woldlab/castor/home/georgi/programs/CISA1.3/src/CISA1/Controllor_R1.pyR)   (   s    	(   t   __name__t
   __module__R   R   R(   R)   (    (    (    sG   /woldlab/castor/home/georgi/programs/CISA1.3/src/CISA1/Controllor_R1.pyR      s   			(    (   R   t   ost   filecmpt   Auto_RunR    R   (    (    (    sG   /woldlab/castor/home/georgi/programs/CISA1.3/src/CISA1/Controllor_R1.pyt   <module>   s   