Package Bio :: Package SearchIO :: Package BlastIO :: Module blast_xml :: Class BlastXmlParser
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Class BlastXmlParser

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object --+
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        BlastXmlParser

Parser for the BLAST XML format.
Instance Methods [hide private]
 
__init__(self, handle, use_raw_query_ids=False, use_raw_hit_ids=False)
Initialize the class.
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__iter__(self) source code
 
_parse_preamble(self)
Parse all tag data prior to the first query result (PRIVATE).
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_parse_qresult(self)
Parse query results (PRIVATE).
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_parse_hit(self, root_hit_elem, query_id)
Yield a generator object that transforms Iteration_hits XML elements into Hit objects (PRIVATE).
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_parse_hsp(self, root_hsp_frag_elem, query_id, hit_id)
Yield a generator object that transforms Hit_hsps XML elements into HSP objects (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, use_raw_query_ids=False, use_raw_hit_ids=False)
(Constructor)

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Initialize the class.
Overrides: object.__init__

_parse_hit(self, root_hit_elem, query_id)

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Yield a generator object that transforms Iteration_hits XML elements into Hit objects (PRIVATE).
Parameters:
  • root_hit_elem (XML element tag) - root element of the Iteration_hits tag.
  • query_id (string) - QueryResult ID of this Hit

_parse_hsp(self, root_hsp_frag_elem, query_id, hit_id)

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Yield a generator object that transforms Hit_hsps XML elements into HSP objects (PRIVATE).
Parameters:
  • root_hsp_frag_elem (XML element tag) - the Hit_hsps tag
  • query_id (string) - query ID
  • hit_id (string) - hit ID