ó
X_Sc           @   sŠ   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 e j f d „  ƒ  YZ	 e
 d k r† e j ƒ  n  d S(   iÿÿÿÿ(   t   *(   t	   phylip_io(   t   StringIONt   test_phylip_ioc           B   sb   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 d	 „  Z RS(
   c         C   sp   t  d ƒ } t j | ƒ } |  j t | ƒ d ƒ |  j | d j d ƒ |  j t | d ƒ d ƒ | j ƒ  d  S(   Ns   phylip_test_1.phyi
   i    t   Cowi   iê   (   t   testdata_streamR   t   readt   assertEqualt   lent   namet   close(   t   selft   ft   seqs(    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt	   test_read2   s    c         C   s)   t  t j ƒ } |  j t t j | ƒ d  S(   N(   R   t   plain_iot   examplet   assertRaisest
   ValueErrorR   R   (   R   R   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   test_parse_plain_fail;   s    	c         C   sŠ   t  d ƒ } t j | ƒ } |  j t | ƒ d ƒ |  j t | d ƒ d ƒ |  j t | d ƒ d ƒ |  j | d j d ƒ | j ƒ  d  S(   Ns   phylip_test_2.phyi   i    i   i   t   CGTTACTCGTTGTCGTTACTt
   Hesperorni(   R   R   R   R   R   t   strR	   R
   (   R   R   R   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   test_parse_phylip_test_2A   s    c         C   s,   t  t j ƒ } |  j t t j | t ƒ d  S(   N(   R   t
   clustal_ioR   R   R   R   R   t   protein_alphabet(   R   R   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   test_parse_clustal_failJ   s    	c         C   sŠ   t  d ƒ } t j | ƒ } |  j t | ƒ d ƒ |  j t | d ƒ d ƒ |  j t | d ƒ d ƒ |  j | d j d ƒ | j ƒ  d  S(   Ns   phylip_test_3.phyi   i    i   i   R   R   (   R   R   R   R   R   R   R	   R
   (   R   R   R   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   test_parse_phylip_test_3P   s    c         C   sŠ   t  d ƒ } t j | ƒ } |  j t | ƒ d ƒ |  j t | d ƒ d ƒ |  j t | d ƒ d ƒ |  j | d j d ƒ | j ƒ  d  S(	   Ns   phylip_test_4.phyi   i    i   i   t   GTGGTGGTGGGCGCCGGCCGTGTGGi   t   ddrasa(   R   R   R   R   R   R   R	   R
   (   R   R   R   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   test_parse_phylip_test_4Y   s    c         C   sŠ   t  d ƒ } t j | ƒ } |  j t | ƒ d ƒ |  j t | d ƒ d ƒ |  j t | d ƒ d ƒ |  j | d j d ƒ | j ƒ  d  S(	   Ns   phylip_test_5.phyi   i    i2   i   t2   GTGGTGGTGGGCGCCGGCCGTGTGGGTGGTGGTGGGCGCCGGCCGTGTGGi   R   (   R   R   R   R   R   R   R	   R
   (   R   R   R   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   test_parse_phylip_test_5c   s    c         C   s3   t  d ƒ } |  j t t j | t ƒ | j ƒ  d  S(   Ns   phylip_test_6.corrupt.phy(   R   R   R   R   R   R   R
   (   R   R   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   test_parse_wrong_phylip_codes_1l   s    	c         C   s3   t  d ƒ } |  j t t j | t ƒ | j ƒ  d  S(   Ns   phylip_test_7.corrupt.phy(   R   R   R   R   R   R   R
   (   R   R   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   test_parse_wrong_phylip_codes_2r   s    	c         C   s‘   t  d ƒ } t j | ƒ } |  j t | ƒ d ƒ |  j t | d ƒ d ƒ |  j t | d d d !ƒ d ƒ |  j | d j d ƒ | j ƒ  d  S(	   Ns   dna.phyi
   i    iÁ  i   t
   ATGGCACACCi   t   Chicken(   R   R   R   R   R   R   R	   R
   (   R   R   R   (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   test_parse_phylip_dnax   s    !(   t   __name__t
   __module__R   R   R   R   R   R   R    R!   R"   R%   (    (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyR   0   s   									
				t   __main__(   t   corebiot   corebio.seqt   corebio.seq_iot   test_corebioR   t   corebio._py3kR   t   unittestt   TestCaseR   R&   t   main(    (    (    sO   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_phylip_io.pyt   <module>&   s   



R