ó
X_Sc           @   sè   d  d l  Td  d l Td  d l Td  d l Td  d l  m Z d  d l m Z d  d l Z d  d l Td  d l	 Td e j
 f d „  ƒ  YZ d e j
 f d „  ƒ  YZ d	 e j
 f d
 „  ƒ  YZ d Z d Z d Z d Z e d k rä e j ƒ  n  d S(   iÿÿÿÿ(   t   *(   t   data(   t   StringIONt   test_AlphabeticArrayc           B   s   e  Z d  „  Z RS(   c         C   s6   t  t t f ƒ } d | d <| d d k s2 t ‚ d  S(	   Ni
   t   At   Ci    i   g      $@(   R   R   (   i    i   (   t   AlphabeticArrayt   protein_alphabett   AssertionError(   t   selft   matrix(    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_create   s    
(   t   __name__t
   __module__R   (    (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyR      s   t
   test_Motifc           B   s5   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z RS(   c         C   s  t  d ƒ } t j | ƒ } | j ƒ  | d d k s; t ‚ | d d k sQ t ‚ t | j ƒ d k sl t ‚ | j ƒ  t  d
 ƒ } t j | ƒ } | j ƒ  | d d k s± t ‚ | d d k sÇ t ‚ t | j ƒ d k sâ t ‚ t  d ƒ } t j | ƒ } | j ƒ  d  S(   Ns   transfac_matrix.txti   R   g        i    t   Gg       @i   i   s   transfac_matrix2.txtg      @g      c@i   s   transfac_matrix3.txt(   i   R   (   i    R   (   i   i   (   i   R   (   i    R   (   i   i   (   t   testdata_streamt   Motift   read_transfact   closeR   t   shapet   array(   R	   t   ft   m(    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_read_transfac   s     


c         C   s°   t  d ƒ } t j | ƒ } | j ƒ  | j d ƒ } t | j ƒ d k sO t ‚ xZ t d d ƒ D]I } x@ t	 d ƒ D]2 \ } } | | | f | | | f k sr t ‚ qr Wq_ Wd  S(   Ns   transfac_matrix.txtt   TCGAi    i   t   AGCT(
   R   R   R   R   t   reindext   strt   alphabetR   t   ranget	   enumerate(   R	   R   R   t   m2t   kt   it   a(    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_reindex/   s    
c   	      C   sÌ   t  d ƒ } t j | ƒ } t  d ƒ } t j | ƒ } | j ƒ  t | ƒ \ } } x_ t d | ƒ D]N } xE t d | ƒ D]4 } | | | f | | | d | f k sx t ‚ qx Wqb W| j ƒ  | j ƒ  d  S(   Ns   transfac_matrix.txti    i   (   R   R   R   t   reverseR   R   R   R   (	   R	   R   R   t   f2R    t   Kt   NR!   t   n(    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_reverse<   s    
6
c         C   s  t  d ƒ } t j | ƒ } t  d ƒ } t j | ƒ } | j ƒ  t | ƒ \ } } x¯ t d | ƒ D]ž } | | d f | | d f k sŽ t ‚ | | d f | | d f k s´ t ‚ | | d f | | d f k sÚ t ‚ | | d f | | d f k sb t ‚ qb W| j ƒ  | j ƒ  d  S(   Ns   transfac_matrix.txti    R   t   TR   R   (   R   R   R   t
   complementR   R   R   R   (   R	   R   R   R&   R    R'   R(   R!   (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_complementL   s    
&&&*
c         C   sŠ   t  d ƒ } t j | ƒ } t  d ƒ } t j | ƒ } | j ƒ  | j ƒ  | j ƒ  | j | j k j ƒ  sr t ‚ | j	 ƒ  | j	 ƒ  d  S(   Ns   transfac_matrix.txt(
   R   R   R   R,   R%   t   reverse_complementR   t   allR   R   (   R	   R   R   R&   R    (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_reverse_complement\   s    



(   R   R   R   R$   R*   R-   R0   (    (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyR      s
   				t   test_SubMatrixc           B   st   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 d	 „  Z d
 „  Z d „  Z RS(   c         C   sÃ   d } t  d d d d g d d d d	 g d
 d d d g d d d d g g ƒ } t | | ƒ } | d d k ss t ‚ | d d k s‰ t ‚ | d d k sŸ t ‚ d | d <| d d k s¿ t ‚ d  S(   Nt   ABCDi   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   i    R   t   BR   iÿÿÿÿ(   i    i    (   R   R   (   R3   R   (   R3   R   (   R3   R   (   t   asarrayt	   SubMatrixR   (   R	   t   abt   art   s(    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyR   p   s    H
c         C   sè   t  d ƒ } t d d d d g d d d d	 g d
 d d d g d d d d g g ƒ } t | | ƒ } d } d } | j | | f ƒ } x] t | ƒ D]O \ } } x@ t | ƒ D]2 \ }	 }
 | | |
 f | | |	 f k sª t ‚ qª Wq‘ Wd  S(   NR2   i   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   t	   DCCBBBAAAt   BA(   t   AlphabetR4   R5   t   indexR   R   (   R	   R6   R7   R8   t   s1t   s2t   vR   R"   R)   t   j(    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_get{   s    Hc         C   sE  t  d ƒ } t d d d d g d d d d	 g d
 d d d g d d d d g g ƒ } t | | ƒ } | j d ƒ } t | j t d d d g d d d g d
 d d g g ƒ k ƒ s· t ‚ | j d ƒ } t | j t d d g d d g g ƒ k ƒ sù t ‚ | j t  d ƒ ƒ } t | j t d d g d d g g ƒ k ƒ sAt ‚ d  S(   NR2   i   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   t   ABCR:   (   R;   R4   R5   R   R/   R   R   (   R	   R6   R7   t   matt   mat2(    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_get_subMatrix‡   s    HE3c         C   s©   t  d ƒ } t d d d d g d d d d	 g d
 d d d g d d d d g g ƒ } t | | ƒ } |  j t | j d ƒ |  j t | j d ƒ |  j t | j d ƒ d  S(   NR2   i   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   t   ER   t   5t   6(   RF   R   (   RG   RH   (   RF   R   (   R;   R4   R5   t   assertRaisest
   IndexErrort   __getitem__R<   (   R	   R6   R7   R8   (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_fail_get–   s    Hc         C   ss   t  d ƒ } t d d d d g d d d d	 g d
 d d d g d d d d g g ƒ } t | | ƒ } t | ƒ } d  S(   NR2   i   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   (   R;   R4   R5   t   repr(   R	   R6   R7   R8   t   string(    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt	   test_repr¡   s    Hc         C   s5   t  t ƒ } t j | ƒ } | d d k s1 t ‚ d  S(   NR#   i   (   R#   R#   (   R   t   test_matrix1R5   t   readR   (   R	   R   RC   (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt	   test_readª   s    c         C   s&   t  t ƒ } |  j t t j | ƒ d  S(   N(   R   t   test_matrix4RI   t
   ValueErrorR5   RQ   (   R	   R   (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_read_asymmetric_fail¯   s    c         C   sr   t  t ƒ } |  j t t j | ƒ t  t ƒ } t j | d t d ƒ ƒ} t  t ƒ } |  j t t j | t ƒ d  S(   NR   t   ARNDCQEGHILKMFPSTWYV(	   R   t   test_matrix3RI   RT   R5   RQ   R;   RP   t   unambiguous_protein_alphabet(   R	   R   RC   R&   (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_read_alphabets³   s    		c         C   s&   t  t ƒ } |  j t t j | ƒ d  S(   N(   R   t   test_matrix2RI   RT   R5   RQ   (   R	   R   (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_read_corruptÁ   s    	c         C   s|   t  j d ƒ } t j | ƒ } |  j | d d ƒ | j ƒ  t  j d ƒ } t j | ƒ } |  j | d	 d ƒ | j ƒ  d  S(
   Nt   pam250i    g       @t   pam120i   i   iùÿÿÿ(   i    i    (   i   i   (   R   t   data_streamR5   RQ   t   assertEqualR   (   R	   R   RC   (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_read_pamÆ   s    
c         C   s|   t  j d ƒ } t j | ƒ } |  j | d	 d ƒ | j ƒ  t  j d ƒ } t j | ƒ } |  j | d
 d ƒ | j ƒ  d  S(   Nt   blosum80i    i
   iýÿÿÿt   blosum62i   i   iüÿÿÿ(   i    i
   (   i   i   (   R   R^   R5   RQ   R_   R   (   R	   R   RC   (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_read_blosumÑ   s    
c         C   sÅ   t  d ƒ } t j | ƒ } |  j | d d ƒ | j ƒ  t  d ƒ } t j | ƒ } |  j | d d ƒ |  j | j j d ƒ | j ƒ  t  d
 ƒ } t j | ƒ } |  j | d d ƒ | j ƒ  d  S(   Ns   blosum35.blast.newi   i   iýÿÿÿs   blosum35.blasti    i
   iþÿÿÿi   s
   pam250.matiûÿÿÿ(   i   i   (   i    i
   (   i   i   (   i   i   (   R   R5   RQ   R_   R   R   R   (   R	   R   RC   (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   test_read_blastÜ   s    

(   R   R   R   RA   RE   RL   RO   RR   RU   RY   R[   R`   Rc   Rd   (    (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyR1   n   s   												sÎ  # A Test Matrix
# More comments

# And blank line should be ignored

A    4  -2  -2  -2   0  -1  -1  -1  -2  -2  -2  -2  -1  -2  -1   0  -1  -3  -2  -1  -2  -1  -1
R   -2   6  -1  -1  -4   1   0  -3   0  -3  -3   2  -2  -3  -2  -1  -1  -2  -2  -3   3  -1  -1
N   -2  -1   7   1  -3   0   0  -1   0  -5  -4   0  -3  -4  -2   0  -1  -3  -2  -4   3  -1  -1
D   -2  -1   1   7  -4   0   1  -1  -1  -6  -5   0  -4  -5  -1   0  -1  -4  -3  -5   0  -2  -2
C    0  -4  -3  -4  12  -3  -4  -3  -3  -1  -2  -4  -1  -2  -3  -2  -1  -2  -2   0  -3   5  -2
Q   -1   1   0   0  -3   6   1  -2   0  -3  -3   1  -2  -3  -1   0  -1  -2  -2  -3   0   1  -1
E   -1   0   0   1  -4   1   5  -2  -1  -4  -4   1  -3  -4  -1  -1  -1  -3  -3  -4   0  -1  -1
G   -1  -3  -1  -1  -3  -2  -2   7  -2  -6  -5  -2  -4  -5  -2  -1  -2  -4  -4  -5  -2  -2  -2
H   -2   0   0  -1  -3   0  -1  -2   9  -3  -3  -1  -2  -1  -2  -1  -1   0   0  -3   0  -1  -1
I   -2  -3  -5  -6  -1  -3  -4  -6  -3   5   2  -4   1   0  -4  -4  -2  -1  -1   3  -4  -2  -2
L   -2  -3  -4  -5  -2  -3  -4  -5  -3   2   5  -3   2   1  -3  -3  -2  -1  -1   1  -4  -2  -2
K   -2   2   0   0  -4   1   1  -2  -1  -4  -3   5  -2  -4  -1  -1  -1  -3  -3  -3   1  -1  -1
M   -1  -2  -3  -4  -1  -2  -3  -4  -2   1   2  -2   7   1  -3  -2  -1   0   0   1  -3  -2  -1
F   -2  -3  -4  -5  -2  -3  -4  -5  -1   0   1  -4   1   7  -3  -3  -2   3   3   0  -3  -2  -1
P   -1  -2  -2  -1  -3  -1  -1  -2  -2  -4  -3  -1  -3  -3   8  -1  -2  -3  -3  -3  -2  -2  -2
S    0  -1   0   0  -2   0  -1  -1  -1  -4  -3  -1  -2  -3  -1   4   1  -3  -2  -3   0  -1  -1
T   -1  -1  -1  -1  -1  -1  -1  -2  -1  -2  -2  -1  -1  -2  -2   1   5  -2  -2  -1  -1  -1  -1
W   -3  -2  -3  -4  -2  -2  -3  -4   0  -1  -1  -3   0   3  -3  -3  -2  12   3  -2  -3  -2  -1
Y   -2  -2  -2  -3  -2  -2  -3  -4   0  -1  -1  -3   0   3  -3  -2  -2   3   8  -2  -2  -2  -1
V   -1  -3  -4  -5   0  -3  -4  -5  -3   3   1  -3   1   0  -3  -3  -1  -2  -2   5  -4  -2  -2
B   -2   3   3   0  -3   0   0  -2   0  -4  -4   1  -3  -3  -2   0  -1  -3  -2  -4   3  -1  -1
Z   -1  -1  -1  -2   5   1  -1  -2  -1  -2  -2  -1  -2  -2  -2  -1  -1  -2  -2  -2  -1   3  -1
X   -1  -1  -1  -2  -2  -1  -1  -2  -1  -2  -2  -1  -1  -1  -2  -1  -1  -1  -1  -2  -1  -1  -1
s	  # An invalid Test Matrix
# Its got a non-numerical value in it. Is the correct exception raised?

# And blank line should be ignored

A    4  -2  -2  -2   0  -1  -1  -1  -2  -2  -2  -2  -1  -2  -1   0  -1  -3  -2  -1  -2  -1  -1
R   -2   6  -1  -1  -4   1   0  -3   0  -3  -3   2  -2  -3  -2  -1  -1  -2  -2  -3   3  -1  -1
N   -2  -1   7   1  -3   0   0  -1   0  -5  -4   0  -3  -4  -2   0  -1  -3  -2  -4   3  -1  -1
D   -2  -1   1   7  -4   0   1  -1  -1  -6  -5   0  -4  -5  -1   0  -1  -4  -3  -5   0  -2  -2
C    0  -4  -3  -4  12  -3  -4  -3  -3  -1  -2  -4  -1  -2  -3  -2  -1  -2  -2   0  -3   5  -2
Q   -1   1   0   0  -3   6   1  -2   0  -3  -3   1  -2  -3  -1   0  -1  -2  -2  -3   0   1  -1
E   -1   0   0   1  -4   x   5  -2  -1  -4  -4   1  -3  -4  -1  -1  -1  -3  -3  -4   0  -1  -1
G   -1  -3  -1  -1  -3  -2  -2   7  -2  -6  -5  -2  -4  -5  -2  -1  -2  -4  -4  -5  -2  -2  -2
H   -2   0   0  -1  -3   0  -1  -2   9  -3  -3  -1  -2  -1  -2  -1  -1   0   0  -3   0  -1  -1
I   -2  -3  -5  -6  -1  -3  -4  -6  -3   5   2  -4   1   0  -4  -4  -2  -1  -1   3  -4  -2  -2
L   -2  -3  -4  -5  -2  -3  -4  -5  -3   2   5  -3   2   1  -3  -3  -2  -1  -1   1  -4  -2  -2
K   -2   2   0   0  -4   1   1  -2  -1  -4  -3   5  -2  -4  -1  -1  -1  -3  -3  -3   1  -1  -1
M   -1  -2  -3  -4  -1  -2  -3  -4  -2   1   2  -2   7   1  -3  -2  -1   0   0   1  -3  -2  -1
F   -2  -3  -4  -5  -2  -3  -4  -5  -1   0   1  -4   1   7  -3  -3  -2   3   3   0  -3  -2  -1
P   -1  -2  -2  -1  -3  -1  -1  -2  -2  -4  -3  -1  -3  -3   8  -1  -2  -3  -3  -3  -2  -2  -2
S    0  -1   0   0  -2   0  -1  -1  -1  -4  -3  -1  -2  -3  -1   4   1  -3  -2  -3   0  -1  -1
T   -1  -1  -1  -1  -1  -1  -1  -2  -1  -2  -2  -1  -1  -2  -2   1   5  -2  -2  -1  -1  -1  -1
W   -3  -2  -3  -4  -2  -2  -3  -4   0  -1  -1  -3   0   3  -3  -3  -2  12   3  -2  -3  -2  -1
Y   -2  -2  -2  -3  -2  -2  -3  -4   0  -1  -1  -3   0   3  -3  -2  -2   3   8  -2  -2  -2  -1
V   -1  -3  -4  -5   0  -3  -4  -5  -3   3   1  -3   1   0  -3  -3  -1  -2  -2   5  -4  -2  -2
B   -2   3   3   0  -3   0   0  -2   0  -4  -4   1  -3  -3  -2   0  -1  -3  -2  -4   3  -1  -1
Z   -1  -1  -1  -2   5   1  -1  -2  -1  -2  -2  -1  -2  -2  -2  -1  -1  -2  -2  -2  -1   3  -1
X   -1  -1  -1  -2  -2  -1  -1  -2  -1  -2  -2  -1  -1  -1  -2  -1  -1  -1  -1  -2  -1  -1  -1
sÐ  #
# This test matrix has a smaller alphabet
A    4  -2  -2  -2   0  -1  -1  -1  -2  -2  -2  -2  -1  -2  -1   0  -1  -3  -2  -1  
R   -2   6  -1  -1  -4   1   0  -3   0  -3  -3   2  -2  -3  -2  -1  -1  -2  -2  -3  
N   -2  -1   7   1  -3   0   0  -1   0  -5  -4   0  -3  -4  -2   0  -1  -3  -2  -4  
D   -2  -1   1   7  -4   0   1  -1  -1  -6  -5   0  -4  -5  -1   0  -1  -4  -3  -5  
C    0  -4  -3  -4  12  -3  -4  -3  -3  -1  -2  -4  -1  -2  -3  -2  -1  -2  -2   0  
Q   -1   1   0   0  -3   6   4  -2   0  -3  -3   1  -2  -3  -1   0  -1  -2  -2  -3  
E   -1   0   0   1  -4   4   5  -2  -1  -4  -4   1  -3  -4  -1  -1  -1  -3  -3  -4  
G   -1  -3  -1  -1  -3  -2  -2   7  -2  -6  -5  -2  -4  -5  -2  -1  -2  -4  -4  -5  
H   -2   0   0  -1  -3   0  -1  -2   9  -3  -3  -1  -2  -1  -2  -1  -1   0   0  -3  
I   -2  -3  -5  -6  -1  -3  -4  -6  -3   5   2  -4   1   0  -4  -4  -2  -1  -1   3  
L   -2  -3  -4  -5  -2  -3  -4  -5  -3   2   5  -3   2   1  -3  -3  -2  -1  -1   1  
K   -2   2   0   0  -4   1   1  -2  -1  -4  -3   5  -2  -4  -1  -1  -1  -3  -3  -3  
M   -1  -2  -3  -4  -1  -2  -3  -4  -2   1   2  -2   7   1  -3  -2  -1   0   0   1  
F   -2  -3  -4  -5  -2  -3  -4  -5  -1   0   1  -4   1   7  -3  -3  -2   3   3   0  
P   -1  -2  -2  -1  -3  -1  -1  -2  -2  -4  -3  -1  -3  -3   8  -1  -2  -3  -3  -3  
S    0  -1   0   0  -2   0  -1  -1  -1  -4  -3  -1  -2  -3  -1   4   1  -3  -2  -3  
T   -1  -1  -1  -1  -1  -1  -1  -2  -1  -2  -2  -1  -1  -2  -2   1   5  -2  -2  -1  
W   -3  -2  -3  -4  -2  -2  -3  -4   0  -1  -1  -3   0   3  -3  -3  -2  12   3  -2  
Y   -2  -2  -2  -3  -2  -2  -3  -4   0  -1  -1  -3   0   3  -3  -2  -2   3   8  -2  
V   -1  -3  -4  -5   0  -3  -4  -5  -3   3   1  -3   1   0  -3  -3  -1  -2  -2   5  
sÅ  # This matrix is invalid because it is asymetric! (AR, RA)

A    4   2  -2  -2   0  -1  -1  -1  -2  -2  -2  -2  -1  -2  -1   0  -1  -3  -2  -1  -2  -1  -1
R   -2   6  -1  -1  -4   1   0  -3   0  -3  -3   2  -2  -3  -2  -1  -1  -2  -2  -3   3  -1  -1
N   -2  -1   7   1  -3   0   0  -1   0  -5  -4   0  -3  -4  -2   0  -1  -3  -2  -4   3  -1  -1
D   -2  -1   1   7  -4   0   1  -1  -1  -6  -5   0  -4  -5  -1   0  -1  -4  -3  -5   0  -2  -2
C    0  -4  -3  -4  12  -3  -4  -3  -3  -1  -2  -4  -1  -2  -3  -2  -1  -2  -2   0  -3   5  -2
Q   -1   1   0   0  -3   6   1  -2   0  -3  -3   1  -2  -3  -1   0  -1  -2  -2  -3   0   1  -1
E   -1   0   0   1  -4   1   5  -2  -1  -4  -4   1  -3  -4  -1  -1  -1  -3  -3  -4   0  -1  -1
G   -1  -3  -1  -1  -3  -2  -2   7  -2  -6  -5  -2  -4  -5  -2  -1  -2  -4  -4  -5  -2  -2  -2
H   -2   0   0  -1  -3   0  -1  -2   9  -3  -3  -1  -2  -1  -2  -1  -1   0   0  -3   0  -1  -1
I   -2  -3  -5  -6  -1  -3  -4  -6  -3   5   2  -4   1   0  -4  -4  -2  -1  -1   3  -4  -2  -2
L   -2  -3  -4  -5  -2  -3  -4  -5  -3   2   5  -3   2   1  -3  -3  -2  -1  -1   1  -4  -2  -2
K   -2   2   0   0  -4   1   1  -2  -1  -4  -3   5  -2  -4  -1  -1  -1  -3  -3  -3   1  -1  -1
M   -1  -2  -3  -4  -1  -2  -3  -4  -2   1   2  -2   7   1  -3  -2  -1   0   0   1  -3  -2  -1
F   -2  -3  -4  -5  -2  -3  -4  -5  -1   0   1  -4   1   7  -3  -3  -2   3   3   0  -3  -2  -1
P   -1  -2  -2  -1  -3  -1  -1  -2  -2  -4  -3  -1  -3  -3   8  -1  -2  -3  -3  -3  -2  -2  -2
S    0  -1   0   0  -2   0  -1  -1  -1  -4  -3  -1  -2  -3  -1   4   1  -3  -2  -3   0  -1  -1
T   -1  -1  -1  -1  -1  -1  -1  -2  -1  -2  -2  -1  -1  -2  -2   1   5  -2  -2  -1  -1  -1  -1
W   -3  -2  -3  -4  -2  -2  -3  -4   0  -1  -1  -3   0   3  -3  -3  -2  12   3  -2  -3  -2  -1
Y   -2  -2  -2  -3  -2  -2  -3  -4   0  -1  -1  -3   0   3  -3  -2  -2   3   8  -2  -2  -2  -1
V   -1  -3  -4  -5   0  -3  -4  -5  -3   3   1  -3   1   0  -3  -3  -1  -2  -2   5  -4  -2  -2
B   -2   3   3   0  -3   0   0  -2   0  -4  -4   1  -3  -3  -2   0  -1  -3  -2  -4   3  -1  -1
Z   -1  -1  -1  -2   5   1  -1  -2  -1  -2  -2  -1  -2  -2  -2  -1  -1  -2  -2  -2  -1   3  -1
X   -1  -1  -1  -2  -2  -1  -1  -2  -1  -2  -2  -1  -1  -1  -2  -1  -1  -1  -1  -2  -1  -1  -1
t   __main__(   t   corebiot   corebio.matrixt   corebio.seqt   corebio.utilsR   t   corebio._py3kR   t   unittestt   numpyt   test_corebiot   TestCaseR   R   R1   RP   RZ   RW   RS   R   t   main(    (    (    sL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyt   <module>   s"   

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