ķ
gbc           @   sŪ   d  d l  m Z d  d l Z d  d l Z d  d l Z d  d l m Z d  d l m Z m	 Z	 d  d l m
 Z
 m Z d  d l m Z d e f d     YZ d	 e f d
     YZ d e f d     YZ d d  Z d d  Z d S(   i˙˙˙˙(   t   urlopenN(   t   EFetch(   t   genbankParsert   genpepParser(   t   genbankIteratort   genpepIterator(   t   CachedDBt   NCBIGenbankc           B   s   e  Z d    Z d   Z RS(   c         C   s   t  j |  d d d d d  S(   Nt   dbt
   nucleotidet   rettypet   gbwithparts(   R   t   __init__(   t   self(    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyR      s    c         C   s|   t  | t  r1 |  j d |  } t |  } | Sd j g  | D] } | ^ q>  } t j |  j d |   } t |  Sd  S(   Nt   idt   ,(   t
   isinstancet   strt   getR   t   joint	   cStringIOt   StringIOR   (   R   t   act   textt   seqt   xt   queryt   data(    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyt   __getitem__   s    "(   t   __name__t
   __module__R   R   (    (    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyR      s   	t
   NCBIGenpepc           B   s   e  Z d    Z d   Z RS(   c         C   s   t  j |  d d d d d  S(   NR   t   proteinR
   R   (   R   R   (   R   (    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyR   !   s    c         C   s|   t  | t  r1 |  j d |  } t |  } | Sd j g  | D] } | ^ q>  } t j |  j d |   } t |  Sd  S(   NR   R   (   R   R   R   R   R   R   R   R   (   R   R   R   R   R   R   R   (    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyR   %   s    "(   R   R   R   R   (    (    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyR       s   	t   NCBIAccessionc           B   s)   e  Z e j d   Z d   Z d   Z RS(   s    +accession +"([^"]+)"c         C   s   t  j |  d d d d d  S(   NR   R	   R
   t   seqid(   R   R   (   R   (    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyR   3   s    c         C   s   t  | t  r@ |  j d |  } t j j |  j d  } | Sd j g  | D] } | ^ qM  } |  j d |  } d   t j j |  D } | Sd  S(   NR   i   R   c         s   s   |  ] } | j  d   Vq d S(   i   N(   t   group(   t   .0R   (    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pys	   <genexpr>?   s    (	   R   R   R   R!   t	   _matchACSt   searchR#   R   t   finditer(   R   R   R   t   repR   R   (    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyR   7   s    "(   R   R   t   ret   compileR%   R   R   (    (    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyR!   /   s   	c         C   s+   t    } |  d  k	 r' t |  |  } n  | S(   N(   R   t   NoneR   (   t   cachet   gb(    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyt   GenbankB   s    	c         C   s+   t    } |  d  k	 r' t |  |  } n  | S(   N(   R   R+   R   (   R,   t   gp(    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyt   GenpepI   s    	(   t   urllib2R    t   sysR)   R   t   obitools.eutilsR   t   parserR   R   R   R   t   obitools.utilsR   R   R   R!   R+   R.   R0   (    (    (    s:   lib/python2.7/site-packages/obitools/seqdb/genbank/ncbi.pyt   <module>   s   