
dHc        +   @   s  d  d l  Z  d  d l Z d  d l m Z d  d l m Z d d d d d d	 d
 d d d d d d d d d d d d d d d d d d d d d d  d! d" d# d$ d% d& d' d( d) d* d+ d, d- d. g+ Z d d d	 d d d d d g Z x e j e j	 e j
 g D] Z y7 e d/ d0 d1 d2 d3 dN d6 d7 Z e s2t d8   Wn+ e k
 r`Z e e  d9 k sat  n Xy= e d/ d0 d1 d2 d: d; d3 d< d= d> Z e st d?   Wq e k
 rZ e e  d@ k st  q Xq WdA GHe j   Z xP e D]H Z dB dC GdD e GHe  j j dE e  Z e j e e  e j    qWxP e D]H Z dB dC GdD e GHe  j j dE e  Z e j e e  e j    q;WdF GHe j   Z e j   Z x e D] Z dB dC GdD e GHe  j j dE e  Z y e j  e e   Z! Wqe k
 r>Z" e j# e e"  dG  dH k r8e j  e e   Z! q?  qXqWdI GHe  j j dE e d;  Z e j  e e   Z! dJ GHd  dK l$ m% Z% e! j& j' e% j(  Z) e) j* dH  Z+ e+ j, e% j( k st  e+ j- dL  e! j& j. dH dM k st  d S(O   iN(   t   ParserSupport(   t   NCBIStandalonet   bt001t   bt002t   bt003t   bt004t   bt005t   bt006t   bt007t   bt009t   bt010t   bt011t   bt012t   bt013t   bt014t   bt015t   bt016t   bt017t   bt018t   bt039t   bt040t   bt041t   bt042t   bt043t   bt044t   bt045t   bt046t   bt047t   bt048t   bt049t   bt050t   bt051t   bt052t   bt053t   bt054t   bt055t   bt056t   bt057t   bt058t   bt059t   bt060t   bt062t   bt063t   bt067t   bt071s   /somewhere/blastt   blastzt   nrs   /tmp/example.fastat   expectationi
   it   matrixs   IDENTITY -F 0; cat /etc/passwd's'   Attempted command injection not caught!s(   Rejecting suspicious argument for matrixt   nprocessorsi   s   0.001t   filters   F > /etc/passwd's(   Attempted output redirection not caught!s(   Rejecting suspicious argument for filters   Running tests on _Scannert   *i2   s
   TESTING %st   Blasts   Running tests on BlastParsers   PSI-BLAST datai    s   Running tests on Blast Recordss*   	Testing conversion of multiple alignments(   t   IUPACi<   i   g-C6?(/   t   ost   stringt   BioR    t	   Bio.BlastR   t	   all_testst   detailed_testst   blastallt   blastpgpt   rpsblastt   funct   handlet   Falset   AssertionErrort
   ValueErrort   et   strt   _Scannert   scannert   testt   patht   joint   datafilet   feedt   opent   AbstractConsumert   TaggingConsumert   BlastParsert   parsert   PSIBlastParsert	   pb_parsert   parset   rect   xt   findt   Bio.AlphabetR5   t   multiple_alignmentt
   to_generict   proteint   generic_alignt   get_seq_by_numt   test_seqt   alphabett   datat	   alignment(    (    (    s   test_NCBIStandalone.pyt   <module>   s   				   