ó
X_Sc           @   sˆ   d  d l  Td  d l Td  d l Z d e j f d „  ƒ  YZ d e j f d „  ƒ  YZ d e j f d „  ƒ  YZ e d	 k r„ e j ƒ  n  d S(
   iÿÿÿÿ(   t   *Nt   test_mask_low_complexityc           B   s   e  Z d  „  Z d „  Z RS(   c         C   s¹   d j  ƒ  } d j  ƒ  } t | t ƒ } t | t ƒ } t d t | ƒ t ƒ } t | ƒ } |  j | | ƒ t | d d d ƒ } |  j | | ƒ t | d d d ƒ } |  j | | ƒ d  S(   Ntv   mgnrafkshhghflsaegeavkthhghhdhhthfhvenhggkvalkthcgkylsigdhkqvylshhlhgdhslfhlehhggkvsikghhhhyisadhhghvstkehhdhdttfeeiiitv   MGNRAFKSHHGHFLSAEGEAVxxxxxxxxxxxxxxxENHGGKVALKTHCGKYLSIGDHKQVYLSHHLHGDHSLFHLEHHGGKVSIKGHHHHYISADHHGHVSTKEHHDHDTTFEEIIIt   Xi   i    g333333@(   t   uppert   Seqt   protein_alphabett   lent   mask_low_complexityt   assertEqual(   t   selft   beforet   aftert   bseqt   aseqt   xseqt   sseq(    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyt   test_segging!   s    c         C   sƒ   t  d t ƒ } |  j t t | d d d ƒ |  j t t | d d d ƒ |  j t t | d d d ƒ |  j t t | d d	 d
 ƒ d  S(   Nt   KTHCGKYLSIGDHKQVYLSHHi   iÿÿÿÿi    i   i
   i   i   g       @gffffffþ?(   R   R   t   assertRaisest
   ValueErrorR	   (   R   t   seq(    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyt   test_seg_invalid8   s
    (   t   __name__t
   __module__R   R   (    (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyR       s   	t   test_transformc           B   s   e  Z d  „  Z d „  Z RS(   c         C   sl   t  t d t ƒ t d t ƒ ƒ } t d t ƒ } | | ƒ } |  j | j t ƒ |  j | t d t ƒ ƒ d  S(   Nt   ACGTURYSWKMBDHVNt   ACGTTNNNNNNNNNNNt   AAAAARt   AAAAAN(   t	   TransformR   t   nucleic_alphabett   dna_alphabetR
   t   alphabet(   R   t   transt   s0t   s1(    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyR   A   s    c         C   s6   t  d t ƒ } x  t j ƒ  D] } | | ƒ } q Wd  S(   NtR   ENHGGKVALKTHCGKYLSIGDHKQVYLSHHLHGDHSLFHLEHHGGKVSIKGHHHHYISADHHGHVSTKEHHDHDTTFEEIII(   R   t   reduced_protein_alphabett   reduced_protein_alphabetst   values(   R   R   t   tt   s(    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyt   test_reduced_protein_alphabetsP   s    (   R   R   R   R,   (    (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyR   @   s   	t   test_geneticcodec           B   s,   e  Z d  „  Z d „  Z d „  Z d „  Z RS(   c         C   se   x^ t  j ƒ  D]P } t | ƒ } t | ƒ } |  j | t | ƒ ƒ |  j t | ƒ t | ƒ ƒ q Wd  S(   N(   t   GeneticCodet   std_listt   reprt   evalR
   t   str(   R   R*   t   rt   gc(    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyt	   test_repr[   s
    c         C   sa   d } t  j ƒ  } | j | ƒ } |  j t | ƒ d ƒ x# t  j ƒ  D] } | j | ƒ } qD Wd  S(   Nt!   GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGAs   AIVMGR*KGAR(   R.   t   stdt	   translateR
   R2   R/   (   R   t   dnaR*   R+   t   p(    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyt   test_translate_stde   s    c         C   sa   d	 d
 d f } xK | D]C \ } } } t  j | ƒ } | j | ƒ } |  j t | ƒ | ƒ q Wd  S(   Ns   Vertebrate MitochondrialR6   t   AIVMGRWKGARi   t   CAAGGCGTCGAAYAGCTTCAGGAACAGGACs
   QGVE?LQEQDi   s   AIVMGR*KGAR(   s   Vertebrate Mitochondrials!   GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGAR<   (   i   R=   s
   QGVE?LQEQD(   i   s!   GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGAs   AIVMGR*KGAR(   R.   t   by_nameR8   R
   R2   (   R   t   cftt   codeR9   t   proteint   cR#   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyt   test_translateo   s     	c         C   sO   d } t  j ƒ  } | j d | j | ƒ } |  j | t | j | ƒ ƒ ƒ d  S(   Ns   ACDEFGHIKLMNPQRSTVWY*t   CGA(   R.   R7   t   tablet   back_translateR
   R2   R8   (   R   t   protR*   R+   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyt   test_back_translate   s
    (   R   R   R5   R;   RC   RH   (    (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyR-   Z   s   	
	
	t   __main__(	   t   corebio.transformt   corebio.seqt   unittestt   TestCaseR   R   R-   R   t   main(    (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_transform.pyt   <module>   s   

 .