ó
ÊïLc           @   sm   d  d l  m Z d  d l m Z d d d „  ƒ  YZ d „  Z d „  Z d „  Z d „  Z d	 „  Z	 d
 „  Z
 d S(   iÿÿÿÿ(   t   IUPAC(   t	   MEMEMotift   Recordc           B   s    e  Z d  Z d „  Z d „  Z RS(   s.  The class for holding the results from a MAST run.
    
    A MAST.Record holds data about matches between motifs and sequences.
    The motifs held by the Record are objects of the class MEMEMotif.
    
    Methods:
    get_motif_by_name (motif_name): returns a MEMEMotif with the given
    name.
    c         C   s:   g  |  _  d |  _ d |  _ i  |  _ d  |  _ g  |  _ d  S(   Nt    (   t	   sequencest   versiont   databaset   diagramst   Nonet   alphabett   motifs(   t   self(    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyt   __init__   s    					c         C   s+   x$ |  j  D] } | j | k r
 | Sq
 Wd  S(   N(   R
   t   name(   R   R   t   m(    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyt   get_motif_by_name   s    (   t   __name__t
   __module__t   __doc__R   R   (    (    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyR      s   		c         C   sN   t  ƒ  } t | |  ƒ t | |  ƒ t | |  ƒ t | |  ƒ t | |  ƒ | S(   s   read(handle)(   R   t   __read_versiont   __read_database_and_motifst   __read_section_it   __read_section_iit   __read_section_iii(   t   handlet   record(    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyt   read#   s    	c         C   sJ   x* | D] } d | k r Pq q Wt  d ƒ ‚ | j ƒ  j ƒ  d |  _ d  S(   Ns   MAST versionsC   Improper input file. Does not begin with a line with 'MAST version'i   (   t
   ValueErrort   stript   splitR   (   R   R   t   line(    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyR   1   s
    c         C   s¢  x! | D] } | j  d ƒ r Pq q W| j ƒ  } | j  d ƒ sR t d | ƒ ‚ n  | j ƒ  } d | k r} t d | ƒ ‚ n  | j ƒ  j ƒ  } | d |  _ | d d k r» t j |  _ n | d d	 k rÚ t j	 |  _ n  x | D] } d
 | k rá Pqá qá W| j ƒ  } d | k r&t d | ƒ ‚ n  xu | D]m } | j ƒ  sCPn  | j ƒ  j ƒ  } t
 ƒ  } |  j | _ | d | _ t | d ƒ | _ |  j j | ƒ q-Wd  S(   Ns   DATABASE AND MOTIFSs   ****s#   Line does not start with '****':
%st   DATABASEs$   Line does not contain 'DATABASE':
%si   i   s   (nucleotide)s	   (peptide)s   MOTIF WIDTHs   ----s    Line does not contain '----':
%si    (   t
   startswitht   nextR   R   R   R   R    t   unambiguous_dnaR	   t   proteinR   R   t   intt   lengthR
   t   append(   R   R   R   t   wordst   motif(    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyR   :   s<    	c         C   sñ   x! | D] } | j  d ƒ r Pq q Wx! | D] } | j  d ƒ r+ Pq+ q+ W| j ƒ  } | j  d ƒ sv t d | ƒ ‚ n  xF | D]> } | j ƒ  s“ Pq} | j d  d ƒ \ } } |  j j | ƒ q} W| j ƒ  } | j  d ƒ sí t d | ƒ ‚ n  d  S(   Ns
   SECTION I:s   SEQUENCE NAMEs   ---s"   Line does not start with '---':
%si   s   ****s#   Line does not start with '****':
%s(   R    R!   R   R   R   R   R   R&   (   R   R   R   t   sequencet   description_evalue_length(    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyR   \   s"    c         C   s  x! | D] } | j  d ƒ r Pq q Wx! | D] } | j  d ƒ r+ Pq+ q+ W| j ƒ  } | j  d ƒ sv t d | ƒ ‚ n  xq | D]i } | j ƒ  s“ Pq} | j  d ƒ rÄ | j ƒ  } |  j | c | 7<q} | j ƒ  \ } } } | |  j | <q} W| j ƒ  } | j  d ƒ st d | ƒ ‚ n  d  S(   Ns   SECTION II:s   SEQUENCE NAMEs   ---s"   Line does not start with '---':
%st    s   ****s#   Line does not start with '****':
%s(   R    R!   R   R   R   R   (   R   R   R   t   diagramR)   t   pvalue(    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyR   q   s(    c         C   s‘   x! | D] } | j  d ƒ r Pq q Wx! | D] } | j  d ƒ r+ Pq+ q+ Wx! | D] } | j  d ƒ rO PqO qO Wx | D] } | j ƒ  rs Pqs qs Wd  S(   Ns   SECTION III:s   ****s   *****(   R    R   (   R   R   R   (    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyR   ‰   s    N(    (   t   Bio.AlphabetR    t   Bio.Motif.Parsers.MEMER   R   R   R   R   R   R   R   (    (    (    s7   C:\Python27\Lib\site-packages\Bio\Motif\Parsers\MAST.pyt   <module>   s   				"		