
:>"^4  ã            
   @   s|   d  Z  d d l Z Gd d „  d e ƒ Z Gd d „  d e ƒ Z d d d	 d
 d d d d d d i Z Gd d „  d e ƒ Z d S)z¡A parser for the NCBI blastpgp version 2.2.5 output format.

Currently only supports the '-m 9' option, (table w/ annotations).
Returns a BlastTableRec instance
é    Nc               @   s"   e  Z d  Z d Z d d „  Z d S)ÚBlastTableEntryzAContainer for Blast Table Entry, the field values from the table.c             C   sô   | j  ƒ  } | d j  d ƒ |  _ | d j  d ƒ |  _ t | d ƒ |  _ t | d ƒ |  _ t | d ƒ |  _ t | d ƒ |  _ t | d ƒ t | d	 ƒ f |  _	 t | d
 ƒ t | d ƒ f |  _
 t | d ƒ |  _ t | d ƒ |  _ d S)zInitialize the class.r   ú|é   é   é   é   é   é   é   é   é	   é
   é   N)ÚsplitZqidZsidÚfloatÚpidÚintZali_lenZmisZgapsZq_boundsZs_boundsZe_valueZ	bit_score)ÚselfZin_recZ	bt_fields© r   ú>/tmp/pip-build-ww9dw3qa/biopython/Bio/Blast/ParseBlastTable.pyÚ__init__   s    ##zBlastTableEntry.__init__N)Ú__name__Ú
__module__Ú__qualname__Ú__doc__r   r   r   r   r   r      s   r   c               @   s.   e  Z d  Z d Z d d „  Z d d „  Z d S)ÚBlastTableRecz>Container for Blast Table record, list of Blast Table Entries.c             C   sC   d |  _  d |  _ d |  _ d |  _ d |  _ d |  _ g  |  _ d S)zInitialize the class.N)ÚprogramÚversionÚdateÚ	iterationÚqueryÚdatabaseÚentries)r   r   r   r   r   %   s    						zBlastTableRec.__init__c             C   s   |  j  j | ƒ d S)zAdd entry to Blast Table.N)r"   Úappend)r   Úentryr   r   r   Ú	add_entry/   s    zBlastTableRec.add_entryN)r   r   r   r   r   r%   r   r   r   r   r   "   s   
r   ÚBLASTPr   Z	Iterationr   ZQueryr    ZDatabaser!   ZFieldsÚfieldsc               @   s­   e  Z d  Z d Z d d „  Z d d „  Z e j d d k  rI d d	 „  Z d
 d „  Z	 d d „  Z
 d d „  Z d d „  Z d d „  Z d d „  Z d d „  Z d d „  Z d S)ÚBlastTableReaderz"Reader for the output of blastpgp.c             C   s_   | |  _  |  j  j ƒ  } x% | r? d | k r? |  j  j ƒ  } q W| |  _ d |  _ d |  _ d S)zInitialize the class.r&   r   r   N)ÚhandleÚreadlineÚ
_lookaheadÚ_nÚ
_in_header)r   r)   Úinliner   r   r   r   >   s    			zBlastTableReader.__init__c             C   s«   t  ƒ  |  _ |  j d 7_ |  j } | s. d Sxa | r‘ | d d k ri |  j re |  j | ƒ |  _ q Pn |  j | ƒ d |  _ |  j j ƒ  } q1 W| |  _ d |  _ |  j S)z4Return the next record when iterating over the file.r   Nr   ú#)	r   Útable_recordr,   r+   r-   Ú_consume_headerÚ_consume_entryr)   r*   )r   r.   r   r   r   Ú__next__I   s     						zBlastTableReader.__next__r   r   c             C   s
   |  j  ƒ  S)z8Python 2 style alias for Python 3 style __next__ method.)r3   )r   r   r   r   Únext`   s    zBlastTableReader.nextc             C   s    t  | ƒ } |  j j | ƒ d  S)N)r   r0   r%   )r   r.   Zcurrent_entryr   r   r   r2   d   s    zBlastTableReader._consume_entryc             C   s9   x2 t  D]* } | | k r |  j d t  | | ƒ Sq Wd  S)Nz	_parse_%s)Úreader_keywordsÚ_Parse)r   r.   Úkeywordr   r   r   r1   h   s    z BlastTableReader._consume_headerc             C   sG   | j  ƒ  d d  … \ } } } | |  j _ | |  j _ | |  j _ d S)Nr   )r   r0   r   r   r   )r   r.   r   r   r   r   r   r   Ú_parse_versionm   s
    zBlastTableReader._parse_versionc             C   s    t  | j ƒ  d ƒ |  j _ d S)Nr   r   )r   r   r0   r   )r   r.   r   r   r   Ú_parse_iterationt   s    z!BlastTableReader._parse_iterationc             C   s    | j  ƒ  d d  … |  j _ d S)Nr   r   )r   r0   r    )r   r.   r   r   r   Ú_parse_queryx   s    zBlastTableReader._parse_queryc             C   s   | j  ƒ  d |  j _ d S)Nr   r   )r   r0   r!   )r   r.   r   r   r   Ú_parse_database|   s    z BlastTableReader._parse_databasec             C   s   d S)Nr   r   )r   r.   r   r   r   Ú_parse_fields€   s    zBlastTableReader._parse_fieldsc             C   s   t  |  | ƒ | ƒ S)N)Úgetattr)r   Úmethod_namer.   r   r   r   r6   ƒ   s    zBlastTableReader._ParseN)r   r   r   r   r   r3   ÚsysÚversion_infor4   r2   r1   r8   r9   r:   r;   r<   r6   r   r   r   r   r(   ;   s   r(   )r   r?   Úobjectr   r   r5   r(   r   r   r   r   Ú<module>   s   