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

Class BlastXmlWriter

object --+
         |
        BlastXmlWriter

Stream-based BLAST+ XML Writer.

Instance Methods

[hide private]

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

source code

write_file(self, qresults)
Writes the XML contents to the output handle.

source code

_write_elem_block(self, block_name, map_name, obj, opt_dict={})
Writes sibling XML elements. source code

_write_preamble(self, qresult)
Writes the XML file preamble.

source code

_write_param(self, qresult)
Writes the parameter block of the preamble.

source code

_write_qresults(self, qresults)
Writes QueryResult objects into iteration elements.

source code

_write_hits(self, hits)
Writes Hit objects.

source code

_write_hsps(self, hsps)
Writes HSP objects.

source code

_adjust_output(self, hsp, elem, attr)
Adjusts output to mimic native BLAST+ XML as much as possible.

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)

_write_elem_block(self, block_name, map_name, obj, opt_dict=`{}`)

source code

Writes sibling XML elements.

Arguments:
block_name -- String of common element name prefix.
map_name -- Dictionary name to for mapping element and attribute names.
obj -- Object whose attribute values will be used.
opt_dict -- Dictionary for custom element-attribute mapping.

Class BlastXmlWriter

__init__(self, handle) (Constructor)

_write_elem_block(self, block_name, map_name, obj, opt_dict={})

init(self, handle)
(Constructor)

_write_elem_block(self, block_name, map_name, obj, opt_dict=`{}`)