B
    ‰°bY  ã               @   s2   d Z G dd„ dƒZG dd„ dƒZG dd„ d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
c               @   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   s´   |  ¡ }|d   d¡| _|d   d¡| _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.é    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   ú8lib/python3.7/site-packages/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   s.   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  |¡ 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   c               @   sp   e Zd ZdZddddddœ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d„ Zdd„ ZdS )ÚBlastTableReaderz"Reader for the output of blastpgp.r   r   r    r!   Zfields)ÚBLASTPZ	IterationZQueryZDatabaseZFieldsc             C   sB   || _ | j  ¡ }x|r*d|kr*| j  ¡ }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S xF|rj|d dkrN| jrJ|  |¡| _q^P n|  |¡ d| _| j ¡ }q&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__H   s     
zBlastTableReader.__next__c             C   s   t |ƒ}| j |¡ d S )N)r   r/   r%   )r   r-   Zcurrent_entryr   r   r   r1   ^   s    zBlastTableReader._consume_entryc             C   s2   x,| j D ]"}||kr|  d| j |  |¡S qW d S )Nz	_parse_%s)Úreader_keywordsÚ_Parse)r   r-   Úkeywordr   r   r   r0   b   s    z BlastTableReader._consume_headerc             C   s2   |  ¡ dd … \}}}|| j_|| j_|| j_dS )Nr   )r   r/   r   r   r   )r   r-   r   r   r   r   r   r   Ú_parse_versiong   s
    zBlastTableReader._parse_versionc             C   s   t | ¡ d ƒ| j_dS )Nr   r   )r   r   r/   r   )r   r-   r   r   r   Ú_parse_iterationn   s    z!BlastTableReader._parse_iterationc             C   s   |  ¡ dd … | j_dS )Nr   r   )r   r/   r    )r   r-   r   r   r   Ú_parse_queryr   s    zBlastTableReader._parse_queryc             C   s   |  ¡ d | j_dS )Nr   r   )r   r/   r!   )r   r-   r   r   r   Ú_parse_databasev   s    z BlastTableReader._parse_databasec             C   s   dS )Nr   r   )r   r-   r   r   r   Ú_parse_fieldsz   s    zBlastTableReader._parse_fieldsc             C   s   t | |ƒ|ƒS )N)Úgetattr)r   Úmethod_namer-   r   r   r   r4   }   s    zBlastTableReader._ParseN)r   r   r   r   r3   r   r2   r1   r0   r6   r7   r8   r9   r:   r4   r   r   r   r   r&   2   s    r&   N)r   r   r   r&   r   r   r   r   Ú<module>   s   