
:>"^ë  ã               @   sR   d  Z  d d l m Z m Z d d l m Z Gd d „  d e ƒ Z d d „  Z d S)	zParsing AlignACE output files.é    )ÚMotifÚ	Instances)ÚSeqc               @   s"   e  Z d  Z d Z d d „  Z d S)ÚRecordz*AlignACE record (subclass of Python list).c             C   s   d |  _  d S)zInitialize.N)Ú
parameters)Úself© r   ú8/tmp/pip-build-ww9dw3qa/biopython/Bio/motifs/alignace.pyÚ__init__   s    zRecord.__init__N)Ú__name__Ú
__module__Ú__qualname__Ú__doc__r
   r   r   r   r	   r      s   r   c             C   sr  t  ƒ  } t |  ƒ } | j ƒ  | _ t |  ƒ } | j ƒ  | _ d } d } x |  D]} | j ƒ  } | d k rs qR | d d … d k r• i  | _ qR | d d k rË | j d ƒ d } | j j | ƒ qR d	 | k r| j d	 ƒ \ } } | j ƒ  } | j ƒ  } | | j | <qR | d d
 … d k r6g  | _ qR | d d
 … d k r‡| j ƒ  } | d d k snt	 ‚ t
 | d ƒ } g  }	 qR | d d … d k rüd }
 t |	 |
 ƒ }	 t |
 |	 ƒ } t | j ƒ  d ƒ | _ | | _ | | _ | j | ƒ qR t | j d ƒ ƒ d k r@t | j d ƒ d ƒ } |	 j | ƒ qR d | k r^| j d ƒ } qR t | ƒ ‚ qR W| S)z3Parse an AlignACE format handle as a Record object.NÚ é   ZParar   ú#ú	é   ú=é   ZInputr   é   ZMAPZACGTÚ*z
éÿÿÿÿ)r   ÚnextÚstripÚversionÚcommandr   ÚsplitÚ	sequencesÚappendÚAssertionErrorÚintr   r   ÚfloatÚscoreÚnumberÚmaskÚlenr   Ú
ValueError)ÚhandleÚrecordÚliner%   r$   Zseq_nameZpar_nameZ	par_valueÚwordsZ	instancesZalphabetZmotifÚseqr   r   r	   Úread   sV    				r-   N)	r   Z
Bio.motifsr   r   ZBio.Seqr   Úlistr   r-   r   r   r   r	   Ú<module>   s   