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

Class BlastXmlParser

object --+
         |
        BlastXmlParser

Parser for the BLAST XML format

Instance Methods

[hide private]

__init__(self, handle)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

__iter__(self)

source code

_parse_preamble(self)
Parses all tag data prior to the first query result.

source code

_parse_qresult(self)
Parses query results.

source code

_parse_hit(self, root_hit_elem, query_id)
Generator that transforms Iteration_hits XML elements into Hit objects.

source code

_parse_hsp(self, root_hsp_frag_elem, query_id, hit_id)
Iterator that transforms Hit_hsps XML elements into HSP objects.

source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, handle)
(Constructor)

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

_parse_hit(self, root_hit_elem, query_id)

source code

Generator that transforms Iteration_hits XML elements into Hit objects.

Arguments:
root_hit_elem -- Element object of the Iteration_hits tag.
query_id -- String of QueryResult ID of this Hit

_parse_hsp(self, root_hsp_frag_elem, query_id, hit_id)

source code

Iterator that transforms Hit_hsps XML elements into HSP objects.

Arguments:
root_hsp_frag_elem -- Element object of the Hit_hsps tag.
query_id -- Query ID string.
hit_id -- Hit ID string.

Class BlastXmlParser

__init__(self, handle) (Constructor)

_parse_hit(self, root_hit_elem, query_id)

_parse_hsp(self, root_hsp_frag_elem, query_id, hit_id)

init(self, handle)
(Constructor)