ó
vHÜGc           @   s(  d  Z  d d l Z d d l Z d d l Z d d l Z d d l m Z d d d g Z d Z d Z	 d	 Z
 d
 e j f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ d e f d „  ƒ  YZ e j d ƒ Z d „  Z d „  Z d d d d „ Z d „  Z d „  Z e d k r$e ƒ  e ƒ  n  d S(   s   $Revision: 1.5 $iÿÿÿÿN(   t   Wiset   psws   -ls   -Fs   -gs   -es   -mt   AlignmentColumnFullExceptionc           B   s   e  Z RS(    (   t   __name__t
   __module__(    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyR      s   t	   Alignmentc           B   s   e  Z d  „  Z RS(   c         C   si   y |  d j  | ƒ WnM t k
 r> t j  |  t | ƒ ƒ n' t k
 rd t j  |  t | ƒ ƒ n Xd  S(   Niÿÿÿÿ(   t   appendR   t   listt   AlignmentColumnt
   IndexError(   t   selft   column_unit(    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyR       s    (   R   R   R   (    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyR      s   R   c           B   s,   e  Z d  „  Z d „  Z d „  Z d „  Z RS(   c         C   s"   |  j  d k r | j  |  _  n  d  S(   Nt   SEQUENCE(   t   kind(   R
   R   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyt	   _set_kind)   s    c         C   s>   | j  d k s t ‚ | j |  _ t j |  | j d  g ƒ d  S(   Ni    (   t   unitt   AssertionErrorR   R   t   __init__t   columnt   None(   R
   R   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyR   -   s    c         C   s   d |  j  |  d |  d f S(   Ns
   %s(%s, %s)i    i   (   R   (   R
   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyt   __repr__2   s    c         C   sL   |  d d  k	 r t ‚ n  | j d k s. t ‚ |  j | ƒ | j |  d <d  S(   Ni   (   R   R   R   R   R   R   (   R
   R   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyR   5   s
    	(   R   R   R   R   R   R   (    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyR   (   s   			t
   ColumnUnitc           B   s    e  Z d  „  Z d „  Z e Z RS(   c         C   s   | |  _  | |  _ | |  _ d  S(   N(   R   R   R   (   R
   R   R   R   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyR   ?   s    		c         C   s   d |  j  |  j |  j f S(   Ns"   ColumnUnit(unit=%s, column=%s, %s)(   R   R   R   (   R
   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyt   __str__D   s    (   R   R   R   R   R   (    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyR   >   s   		s1   ^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\] \[(\w+)\]$c         C   sV   t  j |  j ƒ  ƒ } | s d St t | j d ƒ ƒ t | j d ƒ ƒ | j d ƒ ƒ S(   s÷   
    >>> print parse_line("Column 0:")
    None
    >>> parse_line("Unit  0- [  -1-   0] [SEQUENCE]")
    ColumnUnit(unit=0, column=0, SEQUENCE)
    >>> parse_line("Unit  1- [  85-  86] [SEQUENCE]")
    ColumnUnit(unit=1, column=86, SEQUENCE)
    Ni   i   i   (   t   _re_unitt   matcht   rstripR   t   intt   group(   t   lineR   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyt
   parse_lineJ   s    	c         C   sl   t  ƒ  } x\ |  D]T } y t j d r- | Gn  Wn t k
 rA n Xt | ƒ } | r | j | ƒ q q W| S(   s•   
    format

    Column 0:
    Unit  0- [  -1-   0] [SEQUENCE]
    Unit  1- [  85-  86] [SEQUENCE]

    means that seq1[0] == seq2[86] (0-based)
    t   WISE_PY_DEBUG(   R   t   ost   environt   KeyErrorR   R   (   t   iterablet	   alignmentR   R   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyt   parseZ   s    	c         O   s‰   t  } | r# | j t | f ƒ n  | rE | j t t | ƒ f ƒ n  | rg | j t t | ƒ f ƒ n  t j | |  | | Ž } t | ƒ S(   N(	   t   _CMDLINE_PSWt   extendt   _OPTION_SCORESt   _OPTION_GAP_STARTt   strt   _OPTION_GAP_EXTENSIONR    t   alignR$   (   t   pairt   scorest	   gap_startt   gap_extensiont   argst   keywdst   cmdlinet	   temp_file(    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyR+   s   s    c           C   s   t  t j d d !ƒ GHd  S(   Ni   i   (   R+   t   syst   argv(    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyt   mainƒ   s    c          O   s6   d d  l  } d d  l } | j | j t |  | Ž d  S(   Niÿÿÿÿ(   t   doctestR4   t   testmodt   modulesR   (   R0   R1   R7   R4   (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyt   _test†   s    t   __main__(   t   __version__t
   exceptionsR   t   reR4   t   BioR    R%   R(   R*   R'   t	   ExceptionR   R   R   R   t   objectR   t   compileR   R   R$   R   R+   R6   R:   R   (    (    (    s   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Wise/psw.pyt   <module>   s0   					