ó
X_Sc           @   sz   d  d l  Td  d l Td  d l Td  d l Td  d l m Z d  d l Z d e j f d „  ƒ  YZ e	 d k rv e j
 ƒ  n  d S(   iÿÿÿÿ(   t   *(   t   StringIONt   test_clustal_parserc           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   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   clustal.alni   i   t
   CATH_HUMANi‹  (   t   testdata_streamt
   clustal_iot   readt   assertEqualt   lent   namet   close(   t   selft   ft   seqs(    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_clustal(   s    c         C   s\   t  d ƒ } | j ƒ  } d d  l } | j d d | ƒ } t j t | ƒ ƒ } | j ƒ  d  S(   Ns   clustalw2.alniÿÿÿÿs   
s   
(   R   R   t   ret   subR   R   R
   (   R   R   t   sR   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_clustal2_newline0   s    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   clustal_headerless.alni   i   t   O16386_CAEELi   i‰   (   R   R   R   R   R   R	   R
   (   R   R   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_headerless;   s    c         C   s3   t  d ƒ } |  j t t j | t ƒ | j ƒ  d  S(   Ns   clustal.aln(   R   t   assertRaisest
   ValueErrorR   R   t   nucleic_alphabetR
   (   R   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_errorF   s    	c         C   s)   t  d ƒ } t j | ƒ } | j ƒ  d  S(   Ns   clustal181.aln(   R   R   R   R
   (   R   R   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_clustal181L   s    c         C   s,   t  d ƒ } t j | t ƒ } | j ƒ  d  S(   Ns   clustal_glualign.aln(   R   R   R   R   R
   (   R   R   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_clustal_glualignQ   s    c         C   s,   t  d ƒ } t j | t ƒ } | j ƒ  d  S(   Ns   clustalw182.aln(   R   R   R   t   protein_alphabetR
   (   R   R   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_clustalw182V   s    c         C   sB   t  t j ƒ } |  j t t j | t ƒ |  j t t j | ƒ d  S(   N(   R   t   fasta_iot   exampleR   R   R   R   R   (   R   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_fasta_fail[   s
    		c         C   s0   t  d ƒ } |  j t t j | ƒ | j ƒ  d  S(   Ns	   globin.fa(   R   R   R   R   R   R
   (   R   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_fasta_fail2d   s    	c         C   s,   t  t j ƒ } t j | ƒ } | j ƒ  d  S(   N(   R   R   R   R   R
   (   R   R   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_clustal_examplek   s    c         C   sq   t  t j ƒ } t j | ƒ } t  ƒ  } t j | | ƒ | j d ƒ t j | ƒ } |  j | | ƒ | j ƒ  d  S(   Ni    (   R   R   R   R   t   writet   seekR   R
   (   R   R   R   t   foutt   seqs2(    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt
   test_writep   s    	c         C   s3   t  t j ƒ } |  j t t j | ƒ | j ƒ  d  S(   N(   R   t   table_ioR   R   R   R   R   R
   (   R   R   (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   test_parse_table_fail~   s    	(   t   __name__t
   __module__R   R   R   R   R   R   R   R   R    R!   R&   R(   (    (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyR   &   s   												t   __main__(   t   test_corebiot   corebiot   corebio.seqt   corebio.seq_iot   corebio._py3kR   t   unittestt   TestCaseR   R)   t   main(    (    (    sP   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_clustal_io.pyt   <module>   s   



d