
hIc           @   sj   d  d l  Z  d  d l m Z d e  j f d     YZ e d k rf e  j d d  Z e  j d e  n  d S(	   iN(   t   Phdt
   PhdTestOnec           B   s#   e  Z d    Z d   Z d   Z RS(   c         C   s   t  d  |  _ d  S(   Ns   Phd/phd1(   t   opent   handle(   t   self(    (    s   test_Phd.pyt   setUp   s    c         C   s   |  j  j   d  S(   N(   R   t   close(   R   (    (    s   test_Phd.pyt   tearDown
   s    c         C   sM  t  j |  j  } | j   } |  j | j d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d	 d
  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d d  |  j | j d d d  |  j | j d d d  t | j	  d } |  j | j	 d d  |  j | j	 d d  |  j | j	 d d  |  j | j	 d d  |  j | j	 d% d  |  j | j	 d) d  |  j | j	 d, d  |  j | j	 d/ d  |  j | j	 d1 d  |  j | j	 d4 d  |  j | j	 | d) d  |  j | j	 | d% d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d% d  |  j | j	 dC d  |  j | j	 dE d  |  j | j	 dG d  |  j | j	 dI d  |  j | j	 dK d  |  j | j	 dM d  |  j | j	 dO d  |  j | j	 dQ d  |  j | j	 dS d  |  j | j	 dU d  |  j | j
 j   dW  dX  |  j | j
 j   dC dY  |  j | j j   dW  dZ  |  j | j j   dC d[  | j   } t | j	  d } |  j | j d\  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d\  |  j | j d	 d
  |  j | j d d  |  j | j d d  |  j | j d d]  |  j | j d d^  |  j | j d d  |  j | j d d_  |  j | j d d dW  |  j | j d d d`  |  j | j d d d  |  j | j	 d d  |  j | j	 d d  |  j | j	 d d  |  j | j	 d d  |  j | j	 d% d  |  j | j	 d) d  |  j | j	 d, d  |  j | j	 d/ d  |  j | j	 d1 d  |  j | j	 d4 d  |  j | j	 | d) d  |  j | j	 | d% d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d% d  |  j | j	 dC d  |  j | j	 dE d  |  j | j	 dG d  |  j | j	 dI d  |  j | j	 dK d  |  j | j	 dM d  |  j | j	 dO d  |  j | j	 dQ d  |  j | j	 dS d  |  j | j	 dU d  |  j | j
 j   dW  d  |  j | j
 j   dC d  |  j | j j   dW  d  |  j | j j   dC d  | j   } t | j	  d } |  j | j d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d	 d
  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d  |  j | j d d dU  |  j | j d d dU  |  j | j d d d  |  j | j	 d d  |  j | j	 d d  |  j | j	 d d  |  j | j	 d d  |  j | j	 d% d  |  j | j	 d) d  |  j | j	 d, d  |  j | j	 d/ d  |  j | j	 d1 d  |  j | j	 d4 d  |  j | j	 | d) d  |  j | j	 | d% d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d d  |  j | j	 | d% d  |  j | j	 dC d  |  j | j	 dE d  |  j | j	 dG d  |  j | j	 dI d  |  j | j	 dK d  |  j | j	 dM d  |  j | j	 dO d |  j | j	 dQ d |  j | j	 dS d |  j | j	 dU d |  j | j
 j   dW  d  |  j | j
 j   dC d  |  j t | j  d S(  sI   Test to check that record parser parses all records of a contig.
        s   34_222_(80-A03-19).b.ab1t   abi_thumbprinti    t   call_methodt   phredt   chemt   termt   chromat_filet   dyet   bigt   phred_versions
   0.020425.ct   quality_levelsic   t   times   Fri Feb 13 09:16:11 2004t   trace_array_max_indexis*  t   trace_array_min_indext   trace_peak_area_ratiog^)?t   trimi   i   i  i   g?t   ct   9t   6t   tt   18t   10t   26t   19t   38i   t   gt   22t   49i   t   37t   65i   t   28t   76i   t   87i   t   24t   100i	   t   at   108t   11t   5259t   5273t   5286t   5300t   5316t   8t   5323t   5343t   5352t   5366t   5378it   10756it   10764it   10769it   10788it   10803it   10816it   10826it   10840it   10855it   10864i
   t
   ctccgtcggat
   ccaaagcgtgt
   cgtcggaacat
   tatttcggags   425_103_(81-A03-19).g.ab1s   Tue Feb 17 10:31:15 2004in)  gMSt$?i  t   14t   3t   17t   23t   35t   53t   68t   15t   75t   85t   94t   115t   33t   5140t   5156t   25t   5167t   5178t   5193t   16t   5204t   5213t   5230t   5242t   5249t   10489t   10503t   10514t   10516t   10530t   10550t   10566t   10574t   7t   10584t   10599t
   cgggatcccat
   cccagccaagt
   cctgatccgat
   ggggccgccas   425_7_(71-A03-19).b.ab1s   Thu Jan 29 11:46:14 2004i)%  g      Y@t   13t   21t   40t   50t   66t   4728t   4737t   4746t   4756t   4759t   4768t   4775t   4783t   4788t   4794t   9445t   9453t   9462t   9465t   9478t   9483t   9485t   9495t   9504t   nt   0t   9511t
   acataaatcat
   atctgctttnN(   R   R   R   (   R   R   R   (   R   R   R   (   R   R   R   (   R    R!   R"   (   R   R#   R$   (   R   R%   R&   (   R    R%   R'   (   R    R(   R)   (   R*   R!   R+   (   R   R,   R-   (   R   R,   R.   (   R   R   R/   (   R    R   R0   (   R*   R   R1   (   R   R2   R3   (   R   R2   R4   (   R    R2   R5   (   R   R2   R6   (   R   R2   R7   (   R   R2   R8   (   R   R2   R9   (   R*   R2   R:   (   R*   R2   R;   (   R*   R2   R<   (   R    R   R=   (   R   R,   R>   (   R    R,   R?   (   R   R,   R@   (   R    R,   RA   (   R   RF   RG   (   R    RH   R,   (   R    R!   RI   (   R    R   RJ   (   R*   R   RK   (   R   R   RL   (   R   RM   RN   (   R   R2   RO   (   R   R2   RP   (   R*   R   RQ   (   R   RR   RS   (   R   R%   RT   (   R    RU   RV   (   R   R%   RW   (   R   R   RX   (   R*   RY   RZ   (   R*   RM   R[   (   R*   R   R\   (   R*   R   R]   (   R   R2   R^   (   R   R2   R_   (   R   R2   R`   (   R   R2   Ra   (   R*   R2   Rb   (   R    R2   Rc   (   R   R2   Rd   (   R   R   Re   (   R*   R2   Rf   (   R*   Rg   Rh   (   R    Rg   Ri   (   R*   R   Rg   (   R   R   Rn   (   R*   R   Ro   (   R   R   R%   (   R*   R2   RR   (   R*   R2   Rp   (   R*   R   Rq   (   R   R   RK   (   R   R   Rr   (   R*   R   RL   (   R*   R   Rs   (   R   R   Rt   (   R*   R   Ru   (   R*   R2   Rv   (   R   R2   Rw   (   R   R2   Rx   (   R*   R2   Ry   (   R    R   Rz   (   R   R2   R{   (   R    R2   R|   (   R*   R2   R}   (   R   R   R~   (   R   R   R   (   R   R   R   (   R    R   R   (   R   R   R   (   R   R   R   (   R   R2   R   (   R   RG   R   (   R   R   R   (   R    t   parseR   t   nextt   assertEqualt	   file_namet   commentst   assertAlmostEqualt   lent   sitest   seqt   tostringt   seq_trimmedt   assertRaisest   StopIteration(   R   t   recordst   recordt   center(    (    s   test_Phd.pyt   test_check_record_parser   s2   (   t   __name__t
   __module__R   R   R   (    (    (    s   test_Phd.pyR      s   		t   __main__t	   verbosityi   t
   testRunner(	   t   unittestt   Bio.SequencingR    t   TestCaseR   R   t   TextTestRunnert   runnert   main(    (    (    s   test_Phd.pyt   <module>   s
   