ó
Y_Sc           @   s˜   d  d l  Td  d l Td  d l Td  d l m Z d  d l Td  d l Z d  d l Z d Z d Z	 d Z
 d e j f d „  ƒ  YZ e d	 k r” e j ƒ  n  d S(
   iÿÿÿÿ(   t   *(   t   StringIONsÕ  
>SEQUENCE_1
;comment line 1 (optional)
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
;comment line 1 (optional)
;comment line 2 (optional)
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
s%   
>
AAAGTG
>
AAAGCG
>
TGCCCT
>
TGCCTT
s$   
>
AAAGTG
>
AAAGCG

TGCCCT
>
TGCCTT
t   test_fasta_ioc           B   s†   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 d „  Z d „  Z RS(   c         C   s€   t  t j ƒ } t j | ƒ } |  j t | ƒ d ƒ |  j | d j d ƒ |  j | d j d ƒ |  j t | d ƒ d ƒ d  S(   Ni   i    s   Lamprey GLOBIN V - SEA LAMPREYt   Lampreyi   iç   (   R   t   fasta_iot   examplet   readt   assertEqualt   lent   descriptiont   name(   t   selft   ft   seqs(    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt	   test_readQ   s    c         C   s,   t  t j ƒ } |  j t t j | t ƒ d  S(   N(   R   R   R   t   assertRaisest
   ValueErrorR   t   nucleic_alphabet(   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_read_failh   s    c         C   sB   t  d ƒ } t j | t ƒ } |  j t | ƒ d ƒ | j ƒ  d  S(   Ns	   globin.fai8   (   t   testdata_streamR   R   t   protein_alphabetR   R   t   close(   R   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_parse_globinm   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   R   (   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_parse_clustal_failt   s    	c         C   s)   t  t j ƒ } |  j t t j | ƒ d  S(   N(   R   t   plain_ioR   R   R   R   R   (   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_parse_plain_failz   s    	c         C   sg   t  t j ƒ } t j | ƒ } t  ƒ  } t j | | ƒ | j d ƒ t j | ƒ } |  j | | ƒ d  S(   Ni    (   R   R   R   R   t   writet   seekR   (   R   R   R   t   foutt   seqs2(    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_write_seq   s    	c         C   sD   t  t j ƒ } t j | ƒ } d | _ t  ƒ  } t j | | ƒ d  S(   Ns   A description
More description(   R   R   R   R   R	   R   (   R   R   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_write_with_headerŒ   s
    		c         C   ss   t  t ƒ } t j | ƒ } |  j t | ƒ d ƒ |  j | d j d ƒ t ƒ |  j | d j j	 ƒ  d d ƒ d  S(   Ni   i   t   SATVSEIs   comment line 1 (optional)(
   R   t   example_with_optional_commentsR   R   R   R   t
   startswitht   TrueR	   t
   splitlines(   R   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_read_comments•   s    c         C   s‚   t  t ƒ } t j | ƒ } t  ƒ  } t j | | ƒ | j d ƒ t j | ƒ } |  j | | ƒ |  j | d j | d j ƒ d  S(   Ni    i   (   R   R"   R   R   R   R   R   R	   (   R   R   R   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_write_comments   s    	c         C   sN   t  t ƒ } t j | ƒ } |  j t | ƒ d ƒ t  ƒ  } t j | | ƒ d  S(   Ni   (   R   t   example3R   R   R   R   R   (   R   R   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_read_headerless¨   s
    	c         C   s—   t  t j ƒ } t j | ƒ } |  j t | ƒ d ƒ |  j | d j d ƒ |  j | d j d ƒ |  j | d j d ƒ |  j t | d ƒ d ƒ d  S(   Ni   i    s   Lamprey GLOBIN V - SEA LAMPREYR   t   Hagfishiç   (   R   R   R   t   indexR   R   R	   R
   (   R   R   t   idx(    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt
   test_index³   s    c         C   s4   t  ƒ  } t j | ƒ } t | ƒ d k s0 t ‚ d  S(   Ni    (   R   R   R   R   t   AssertionError(   R   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_read_empty½   s    	c         C   sz   t  j t ƒ  ƒ } | j ƒ  s$ t ‚ t  j t t  j ƒ ƒ } | j ƒ  sN t ‚ t  j t t ƒ ƒ } | j ƒ  sv t ‚ d  S(   N(   R   R   R   t	   isalignedR.   R   t   example4(   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_isalignedÂ   s    c         C   sH   t  t ƒ } t j | ƒ } | j ƒ  s. t ‚ |  j t | ƒ d ƒ d  S(   Ni   (   R   R1   R   R   R0   R.   R   R   (   R   R   R   (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   test_read_with_blank_lineÊ   s    (   t   __name__t
   __module__R   R   R   R   R   R   R    R&   R'   R)   R-   R/   R2   R3   (    (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyR   O   s   												
		t   __main__(   t   corebiot   corebio.seqt   corebio.seq_iot   corebio._py3kR   t   test_corebiot   unittestt   timeR"   R(   R1   t   TestCaseR   R4   t   main(    (    (    sN   /Users/gec/Work/Projects/corebioproj/weblogo-3.4/test_corebio/test_fasta_io.pyt   <module>   s   



ƒ