ó
‚™xTc           @   s•   d  d l  m Z d  d l Z d  d l m Z d  d l Z d  d l Z e j j	 d ƒ Z
 d	 d d d „ Z d „  Z e d k r‘ e e j d ƒ n  d S(
   iÿÿÿÿ(   t   divisionN(   t   SorrysÚ  
blast_pdb
  .caption = This program will run a BLAST search on the NCBI's web servers.     You may use any format sequence file, but only a single sequence may be     searched at a time.  (Please limit your use of this service, as it is a     shared public resource!)
  .short_caption = NCBI BLAST search of PDB
  .style = box auto_align caption_img:icons/custom/pdb_import.png
{
  file_name = None
    .type = path
    .style = bold input_file file_type:seq
  output_file = None
    .type = path
    .style = bold new_file
  blast_type = *blastp blastn
    .type = choice
    .caption = Protein_(blastp) Nucleotide_(blastn)
    .short_caption = Search type
  expect = 0.01
    .type = float
    .short_caption = E-value cutoff
}c         C   sm  | d  k r t j } n  | d  k rc d d  l } | j j d |  d t d d ƒ } | j j ƒ  } n  t	 | ƒ | j
 } d d l m } m } d d l m } | | j d d	 d
 t d t ƒ} | j d	 ƒ | j }	 t |	 ƒ d k rô t d ƒ ‚ n t |	 ƒ d k r| d IJn  |	 d j }
 t |
 ƒ d k rAt d ƒ ‚ n! t |
 ƒ d k  rbt d ƒ ‚ n  | j d  k r}d | _ n  | |
 d | j d | j d | j ƒ} | d | j IJ| | ƒ } t |  ƒ d k r4| d IJ| d t | ƒ IJ| d IJ| d IJ| d d IJx | D] } | j | ƒ qWn  t | ƒ d k r_|
 t j j | j ƒ f S|
 d  f Sd  S(   Niÿÿÿÿt   argst   master_philt   seq_file_defs   blast_pdb.file_name(   t   get_ncbi_pdb_blastt   summarize_blast_output(   t   any_filet
   force_typet   seqt"   raise_sorry_if_not_expected_formatt   raise_sorry_if_errorsi    s   Empty sequence file!i   s<   WARNING: multiple sequences provided; searching only the 1sts   No data in sequence file.i   s'   Sequence must be at least six residues.s	   blast.xmlt	   file_namet
   blast_typet   expects   Wrote results to %st    s   %d matching structuress;   ID    Chain     evalue  length  %ident    %pos  #structurest   -i;   (   t   Nonet   syst   stdoutt
   iotbx.philt   philt   process_command_line_with_filesR   t   workt   extractt   validate_paramst	   blast_pdbt   iotbx.bioinformatics.structureR   R   t   iotbx.file_readerR   R   t   Truet   check_file_typet   file_objectt   lenR   t   sequencet   output_fileR   R   t   showt   ost   patht   abspath(   R   t   paramst   outt   iotbxt   cmdlineR   R   R   t   seq_filet   seq_objectsR!   t	   blast_outt   resultst   result(    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/blast_pdb.pyt   run    s^    	
						


c         C   sV   |  j  j d  k r! t d ƒ ‚ n1 t j j |  j  j ƒ sR t d |  j  j ƒ ‚ n  t S(   Ns%   A sequence file is required as input.s   %s is not a file.(   R   R   R   R   R$   R%   t   isfileR   (   R'   (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/blast_pdb.pyR   S   s
    t   __main__i   (    (   t
   __future__R    t   libtbx.philt   libtbxt   libtbx.utilsR   R$   R   R   t   parseR   R   R0   R   t   __name__t   argv(    (    (    sJ   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/command_line/blast_pdb.pyt   <module>   s   		3	