Package Bio :: Package SearchIO :: Package BlastIO :: Module blast_tab :: Class BlastTabParser
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Class BlastTabParser

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object --+
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        BlastTabParser

Parser for the BLAST tabular format.
Instance Methods [hide private]
 
__init__(self, handle, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen'...)
Initialize the class.
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__iter__(self) source code
 
_prep_fields(self, fields)
Validate and format the given fields for use by the parser (PRIVATE).
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_parse_commented_qresult(self)
Yield QueryResult objects from a commented file (PRIVATE).
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_parse_comments(self)
Return a dictionary containing tab file comments (PRIVATE).
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_parse_fields_line(self)
Return column short names line from 'Fields' comment line (PRIVATE).
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_parse_result_row(self)
Return a dictionary of parsed row values (PRIVATE).
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_get_id(self, parsed)
Return the value used for a QueryResult or Hit ID from a parsed row (PRIVATE).
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_parse_qresult(self)
Yield QueryResult objects (PRIVATE).
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_get_frag_frame(self, frag, seq_type, parsedict)
Return fragment frame for given object (PRIVATE).
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_get_frag_strand(self, frag, seq_type, parsedict)
Return fragment strand for given object (PRIVATE).
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, handle, comments=False, fields=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen'...)
(Constructor)

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Initialize the class.
Overrides: object.__init__

_get_frag_frame(self, frag, seq_type, parsedict)

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Return fragment frame for given object (PRIVATE).

Returns HSPFragment frame given the object, its sequence type, and its parsed dictionary values.

_get_frag_strand(self, frag, seq_type, parsedict)

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Return fragment strand for given object (PRIVATE).

Returns HSPFragment strand given the object, its sequence type, and its parsed dictionary values.