l
X_Sc               @   sß   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	 TGd „  d e j
 ƒ Z Gd „  d e j
 ƒ Z Gd	 „  d
 e j
 ƒ Z d Z d Z d Z d Z e d k rÛ e j ƒ  n  d S(   i    (   u   *(   u   data(   u   StringIONc             B   s   |  Ee  Z d  „  Z d S(   c             C   s6   t  t t f ƒ } d | d <| d d k s2 t ‚ d  S(	   Ni
   u   Au   Ci    i   g      $@(   u   Au   C(   i    i   (   u   AlphabeticArrayu   protein_alphabetu   AssertionError(   u   selfu   matrix(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   test_create   s    
N(   u   __name__u
   __module__u   test_create(   u
   __locals__(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   test_AlphabeticArray   s   
u   test_AlphabeticArrayc             B   s;   |  Ee  Z d  „  Z d „  Z d „  Z d „  Z d „  Z d S(   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(   Nu   transfac_matrix.txti   u   Ag        i    u   Gg       @i   i   u   transfac_matrix2.txtg      @g      c@i   u   transfac_matrix3.txt(   i   u   A(   i    u   G(   i   i   (   i   u   A(   i    u   G(   i   i   (   u   testdata_streamu   Motifu   read_transfacu   closeu   AssertionErroru   shapeu   array(   u   selfu   fu   m(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   transfac_matrix.txtu   TCGAi    i   u   AGCT(
   u   testdata_streamu   Motifu   read_transfacu   closeu   reindexu   stru   alphabetu   AssertionErroru   rangeu	   enumerate(   u   selfu   fu   mu   m2u   ku   iu   a(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   transfac_matrix.txti    i   (   u   testdata_streamu   Motifu   read_transfacu   reverseu   shapeu   rangeu   AssertionErroru   close(	   u   selfu   fu   mu   f2u   m2u   Ku   Nu   ku   n(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   transfac_matrix.txti    u   Au   Tu   Gu   C(   u   testdata_streamu   Motifu   read_transfacu
   complementu   shapeu   rangeu   AssertionErroru   close(   u   selfu   fu   mu   f2u   m2u   Ku   Nu   k(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   transfac_matrix.txt(
   u   testdata_streamu   Motifu   read_transfacu
   complementu   reverseu   reverse_complementu   arrayu   allu   AssertionErroru   close(   u   selfu   fu   mu   f2u   m2(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   test_reverse_complement\   s    



N(   u   __name__u
   __module__u   test_read_transfacu   test_reindexu   test_reverseu   test_complementu   test_reverse_complement(   u
   __locals__(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu
   test_Motif   s
   
				u
   test_Motifc             B   sz   |  Ee  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 d S(   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(   Nu   ABCDi   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   i    u   Au   Bu   C(   i    i    (   u   Au   A(   u   Bu   Ciÿÿÿÿ(   u   Bu   C(   u   Bu   Ciÿÿÿÿ(   u   asarrayu	   SubMatrixu   AssertionError(   u   selfu   abu   aru   s(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   test_createp   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(   Nu   ABCDi   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   u	   DCCBBBAAAu   BA(   u   Alphabetu   asarrayu	   SubMatrixu   indexu	   enumerateu   AssertionError(   u   selfu   abu   aru   su   s1u   s2u   vu   mu   iu   nu   j(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   ABCDi   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   u   ABCu   BA(   u   Alphabetu   asarrayu	   SubMatrixu   reindexu   allu   arrayu   AssertionError(   u   selfu   abu   aru   matu   mat2(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   ABCDi   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   u   Eu   Au   5u   6(   u   Eu   A(   u   5u   6(   u   Eu   A(   u   Alphabetu   asarrayu	   SubMatrixu   assertRaisesu
   IndexErroru   __getitem__u   index(   u   selfu   abu   aru   s(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   ABCDi   i   i   i   i   i   i   i   i	   i
   i   i   i   i   i   i   (   u   Alphabetu   asarrayu	   SubMatrixu   repr(   u   selfu   abu   aru   su   string(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu	   test_repr¡   s    Hc             C   s5   t  t ƒ } t j | ƒ } | d d k s1 t ‚ d  S(   Nu   ai   (   u   au   a(   u   StringIOu   test_matrix1u	   SubMatrixu   readu   AssertionError(   u   selfu   fu   mat(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu	   test_readª   s    c             C   s&   t  t ƒ } |  j t t j | ƒ d  S(   N(   u   StringIOu   test_matrix4u   assertRaisesu
   ValueErroru	   SubMatrixu   read(   u   selfu   f(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   alphabetu   ARNDCQEGHILKMFPSTWYV(	   u   StringIOu   test_matrix3u   assertRaisesu
   ValueErroru	   SubMatrixu   readu   Alphabetu   test_matrix1u   unambiguous_protein_alphabet(   u   selfu   fu   matu   f2(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   test_read_alphabets³   s    		c             C   s&   t  t ƒ } |  j t t j | ƒ d  S(   N(   u   StringIOu   test_matrix2u   assertRaisesu
   ValueErroru	   SubMatrixu   read(   u   selfu   f(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   pam250i    g       @u   pam120i   i   i   (   i    i    (   i   i   iùÿÿÿ(   u   datau   data_streamu	   SubMatrixu   readu   assertEqualu   close(   u   selfu   fu   mat(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   blosum80i    i
   i   u   blosum62i   i   (   i    i
   iýÿÿÿ(   i   i   iüÿÿÿ(   u   datau   data_streamu	   SubMatrixu   readu   assertEqualu   close(   u   selfu   fu   mat(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   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(   Nu   blosum35.blast.newi   i   i   u   blosum35.blasti    i
   i   i   u
   pam250.mat(   i   i   iýÿÿÿ(   i    i
   iþÿÿÿ(   i   i   (   i   i   iûÿÿÿ(   u   testdata_streamu	   SubMatrixu   readu   assertEqualu   closeu   arrayu   shape(   u   selfu   fu   mat(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   test_read_blastÜ   s    

N(   u   __name__u
   __module__u   test_createu   test_getu   test_get_subMatrixu   test_fail_getu	   test_repru	   test_readu   test_read_asymmetric_failu   test_read_alphabetsu   test_read_corruptu   test_read_pamu   test_read_blosumu   test_read_blast(   u
   __locals__(    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   test_SubMatrixn   s   
												u   test_SubMatrixuÎ  # 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
u	  # 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
uÐ  #
# 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  
uÅ  # 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
u   __main__(   u   corebiou   corebio.matrixu   corebio.sequ   corebio.utilsu   datau   corebio._py3ku   StringIOu   unittestu   numpyu   test_corebiou   TestCaseu   test_AlphabeticArrayu
   test_Motifu   test_SubMatrixu   test_matrix1u   test_matrix2u   test_matrix3u   test_matrix4u   __name__u   main(    (    (    uL   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_matrix.pyu   <module>   s"   

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
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