ó
{™xTc        4   @   s„  d  d l  m Z d  d l m Z m Z d  d l m Z m Z m Z d  d l m Z d e	 f d „  ƒ  YZ
 e d ƒ Z d „  Z e d	 e d
 d d d ƒ e d
 d d d ƒ e d
 d d d ƒ e d
 d d d ƒ e d
 d d d ƒ e d
 d d d ƒ e d
 d d d d e ƒ g d i d e d	 e d
 d d d ƒ e d
 d d d  d e ƒ e d
 d! d d" d e ƒ e d
 d# d d$ d e ƒ e d
 d% d d& ƒ g ƒ f d' 6d( e d d) d* e d	 e d
 d+ d d, d e ƒ e d
 d d d- d. d/ ƒ e d
 d d d0 d. d/ ƒ e d
 d d d1 d e d. d2 ƒ g d i d3 e d d4 d* e d	 e d
 d+ d d5 d e ƒ e d
 d6 d d7 ƒ e d
 d8 d d9 ƒ e d
 d: d d; d e ƒ e d
 d< d d= d e ƒ g d i d> e d d? d* e d	 e d
 d+ d d@ d e ƒ e d
 dA d dB d e ƒ e d
 dC d dD d e ƒ e d
 dE d dF d e ƒ e d
 dG d	 e d
 dH d dI d e ƒ e d
 dJ d dK d e ƒ e d
 dL d dM d e d. d2 ƒ e d
 dN d dO ƒ g ƒ e d
 dP d	 e d
 dH d dQ d e ƒ e d
 dJ d dR d e ƒ e d
 dL d dS d e d. d2 ƒ e d
 dN d dT ƒ g ƒ e d
 dU d dV d e ƒ e d
 dW d dX d e ƒ e d
 dY d dZ d e d. d2 ƒ e d
 d< d d[ d e ƒ e d
 d\ d d] ƒ g ƒ ƒ f d^ 6ƒ ƒ f d_ 6d` e d	 e d
 da d db d e ƒ e d
 dc d dd d e ƒ e d
 de d df d e ƒ e d
 dg d dh d e ƒ e d
 di d dj d e ƒ e d
 dk d dl d e ƒ e d
 dm d dn d e ƒ g ƒ f do 6ƒ ƒ f dp 6ƒ Z e d dq dr e ds e
 dt e ƒ Z du S(v   iÿÿÿÿ(   t   division(   t   Singlet   Multiple(   t   Textt   TextWithDefaultt   Group(   t   Parsert   Resultc           B   s2   e  Z d  Z d „  Z d „  Z d „  Z d „  Z RS(   s*   
  Homology search by BLAST, XML output
  c         C   s   | |  _  d  S(   N(   t   root(   t   selfR   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ncbi_blast_xml.pyt   __init__   s    c         C   s'   |  j  j r# |  j  j d j | 3n  d  S(   Niÿÿÿÿ(   R   t
   iterationst   hits(   R	   t	   max_count(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ncbi_blast_xml.pyt   restrict   s    c      
   c   s  |  j  j s t ‚ n  d d l m } xî |  j  j d j D]Ù } | j j d ƒ } d t | ƒ k  si t	 ‚ t | ƒ d k rŽ | d } d } n | d  \ } } | j
 d d	 d
 | | f g d | j d j j | j d j j g d d ƒ } | j d | d | d | j d | ƒ Vq9 Wd  S(   Niÿÿÿÿ(   t   bioinformaticst   _i    i   t    i   t   namest   targets   %s_%st
   alignmentst   programs
   NCBI-BLASTt
   identifiert   chaint
   annotationt	   alignment(   R   R   t   StopIterationt   iotbxR   R   t	   accessiont   splitt   lent   AssertionErrort   clustal_alignmentt   hspst   queryt   seqt   hitt   homology_search_hitR   (   R	   R   t   ht   piecest   pdbR   R   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ncbi_blast_xml.pyR      s&    	
		&			c         C   s'   |  j  j s d St |  j  j d j ƒ S(   Ni    iÿÿÿÿ(   R   R   R   R   (   R	   (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ncbi_blast_xml.pyt   __len__6   s    (   t   __name__t
   __module__t   __doc__R
   R   R   R)   (    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ncbi_blast_xml.pyR      s
   			t   -c         C   s   d j  d „  |  Dƒ ƒ S(   NR   c         s   s'   |  ] } | t  k r d  n | Vq d S(   R   N(   t   _alternatives(   t   .0t   c(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ncbi_blast_xml.pys	   <genexpr>B   s    (   t   join(   t   data(    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ncbi_blast_xml.pyt   substitute_underscore@   s    t   extractionst	   attributeR   t   tagt   BlastOutput_programt   versiont   BlastOutput_versiont	   referencet   BlastOutput_referencet   dbt   BlastOutput_dbt   query_ids   BlastOutput_query-IDt	   query_defs   BlastOutput_query-deft	   query_lens   BlastOutput_query-lent
   conversiont   child_data_taggedt
   parameterst   matrixs   Parameters/Parameters_matrixt   expects   Parameters/Parameters_expectt   gap_opens   Parameters/Parameters_gap-opent
   gap_extends    Parameters/Parameters_gap-extendt   filters   Parameters/Parameters_filtert   BlastOutput_paramR   t	   Iterationt	   processort   nums   Iteration_iter-nums   Iteration_query-IDt   defaultR   s   Iteration_query-defs   Iteration_query-leni    R   t   Hitt   Hit_numR   t   Hit_idR   t   Hit_defR   t   Hit_accessiont   lengtht   Hit_lenR!   t   Hspt   Hsp_numt	   bit_scores   Hsp_bit-scoret   scoret	   Hsp_scoret   evaluet
   Hsp_evalueR"   t   starts   Hsp_query-fromt   ends   Hsp_query-tot   frames   Hsp_query-frameR#   t   Hsp_qseqR$   s   Hsp_hit-froms
   Hsp_hit-tos   Hsp_hit-framet   Hsp_hseqt   identityt   Hsp_identityt   positivet   Hsp_positivet   gapst   Hsp_gapss   Hsp_align-lent   midlinet   Hsp_midlinet   Hit_hspst   Iteration_hitst
   statisticst   db_nums   Statistics/Statistics_db-numt   db_lens   Statistics/Statistics_db-lent   hsp_lens   Statistics/Statistics_hsp-lent	   eff_spaces   Statistics/Statistics_eff-spacet   kappas   Statistics/Statistics_kappat   lambdavs   Statistics/Statistics_lambdat   entropys   Statistics/Statistics_entropyt   Iteration_statt   BlastOutput_iterationst   BlastOutputt   buildert   restypet   cElementTreeN(   t
   __future__R    t   iotbx.bioinformatics.xmlbuildR   R   R   R   R   R   t   objectR   t	   frozensetR.   R3   t   intt   floatt   BUILDERt   Truet   parse(    (    (    sQ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/ncbi_blast_xml.pyt   <module>   s¶   7	/
8