Ñò
%WMPc           @   sK   d  d k  Z  d  d k Z d  d k Z d  d k l Z d d d „  ƒ  YZ d S(   iÿÿÿÿN(   t   Get_Info_NUCMert   R1c           B   s,   e  Z d  „  Z d „  Z d „  Z d „  Z RS(   c         C   sX   t  i d | d | ƒ \ } } | GHt  i d | d | d | ƒ \ } } | 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(    (    sO   /sas5t/Oliver/work201403/20140304_CISA_Debug/CISA1.3/src/CISA1/Controllor_R1.pyt   Extend   s    !)c         C   s*   t  i d | d | ƒ \ } } | GHd  S(   Ns   python s   /CISA1/Trim.py (   R   R   (   R   R   R   R	   R
   (    (    sO   /sas5t/Oliver/work201403/20140304_CISA_Debug/CISA1.3/src/CISA1/Controllor_R1.pyt   Trim   s    !c         C   sô  t  | d ƒ } t  | ƒ } t ƒ  } xR t oJ | i ƒ  i d d ƒ } | p Pn | i ƒ  i d d ƒ } | | | <q( Wd } x$ | i ƒ  D] } | t | ƒ 7} q Wx` | D]X }	 |	 i d d ƒ i ƒ  }
 x7 |
 D]/ } | i d | ƒ o | i	 d | ƒ qÓ qÓ Wq® W| i
 ƒ  | i
 ƒ  d } x$ | i ƒ  D] } | t | ƒ 7} q1Wt  | d d ƒ } | i d t | ƒ d ƒ | i d	 t | ƒ d ƒ | i d
 t | ƒ t | ƒ d d ƒ d t | ƒ GHd t | ƒ GHt | ƒ t | ƒ 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(    (    sO   /sas5t/Oliver/work201403/20140304_CISA_Debug/CISA1.3/src/CISA1/Controllor_R1.pyt   Get_explained_info   sD     	      
 
 )c         C   s]   d GHt  ƒ  } | i | | | ƒ |  i | | | ƒ |  i | | ƒ |  i | | ƒ d GHd  S(   Ns	   CISA1....s   CISA1 Done!(   R    t   StartR   R   R(   (   R   t   genome_lR   t   nucmerR   R   t   mywork(    (    sO   /sas5t/Oliver/work201403/20140304_CISA_Debug/CISA1.3/src/CISA1/Controllor_R1.pyR)   (   s    	(   t   __name__t
   __module__R   R   R(   R)   (    (    (    sO   /sas5t/Oliver/work201403/20140304_CISA_Debug/CISA1.3/src/CISA1/Controllor_R1.pyR      s   			(    (   R   t   ost   filecmpt   Auto_RunR    R   (    (    (    sO   /sas5t/Oliver/work201403/20140304_CISA_Debug/CISA1.3/src/CISA1/Controllor_R1.pyt   <module>   s   