ó
gbc           @   s`   d  d l  Z  d  d l Z d  d l m Z d e f d     YZ d d d  Z d d d	  Z d S(
   i˙˙˙˙N(   t   formatFastat   SsearchParserc           B   sW   e  Z e j d  e j  Z e j d e j  Z e j d e j e j  Z d   Z	 RS(   s   ^Query:.+
.+?>+([^ ]+)s   ^Query:.+
.+?(\d+)(?= nt
)s    ^The best scores are:.*
(.+?)>>>c         C   s  t  | t  r! t | d  } n  | j   |  _ t j j |  j  j d  |  _	 t
 t j j |  j  j d   |  _ t j j |  j  } | r~| j d  j d  d d !} g  |  _ xÀ | D]µ } | j d  \ } } | j   } | j   } | d } t
 | d d   } t | d  }	 t t
 | d	  t
 | d
   d }
 |  j j i | d 6|	 d 6| d 6|
 d 6 qÂ Wn  d  S(   Nt   rUi   i    s   
iŝ˙˙˙s   	iû˙˙˙i˙˙˙˙i   i   t   act   identityt   subjectlengtht   matchlength(   t
   isinstancet   strt   opent   readt   dataR   t   _matchQueryt   searcht   groupt   queryt   intt   _matchLQueryt   queryLengtht
   _matchPropt   splitt   propst   floatt   abst   append(   t   selft   fileR   t   linet   subjectt   tabt   sspR   t   dblt   identt   matchlen(    (    s5   lib/python2.7/site-packages/obitools/align/ssearch.pyt   __init__   s*    !'	
((
   t   __name__t
   __module__t   ret   compilet	   MULTILINER   R   t   DOTALLR   R"   (    (    (    s5   lib/python2.7/site-packages/obitools/align/ssearch.pyR      s   t   fasta35t    c         C   sU   t  j d | | | f  \ } } } | t |   IJ| j   t |  } |  | f S(   Ns   %s %s %s(   t   ost   popen3R    t   closeR   (   t   seqt   databaset   programt   optst	   ssearchint
   ssearchoutt
   ssearcherrt   result(    (    s5   lib/python2.7/site-packages/obitools/align/ssearch.pyt   run"   s
    %
t	   ssearch35c         c   s)   x" |  D] } t  | | | |  Vq Wd  S(   N(   R6   (   t   sequenceIteratorR/   R0   R1   R.   (    (    s5   lib/python2.7/site-packages/obitools/align/ssearch.pyt   ssearchIterator*   s    (   R+   R%   t   obitools.fastaR    t   objectR   R6   R9   (    (    (    s5   lib/python2.7/site-packages/obitools/align/ssearch.pyt   <module>   s
   