Package Bio :: Package Ndb
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Package Ndb

source code

This module provided code to parse HTML files from NDB (DEPRECATED).

This module provides an HTML parser designed for the NDB website http://ndbserver.rutgers.edu/ as it was circa 2002. The site has since been redesigned, breaking the parser. Bio.Ndb is therefore deprecated, and will be removed in a future release of Biopython.

Classes: Record Holds NDB sequence data. NdbParser Parses NDB sequence data into a Record object.

The algorithm is based on a state machine because the record has multiple sections and the handling of tags varies depending on the section. Citations have their own state machine.

Classes [hide private]
  Record
  NdbParser
Parses Ndb sequence data into a Record object.
Functions [hide private]
 
_parse_constants(text) source code
Variables [hide private]
  handle = open('PR0004.htm')
  undo_handle = File.UndoHandle(handle)
  ndb_parser = NdbParser()
  record = ndb_parser.parse(handle)
  __package__ = 'Bio.Ndb'
  __warningregistry__ = {('Bio.Ndb has been deprecated as the ND...
  xml_support = 1
Variables Details [hide private]

__warningregistry__

Value:
{('Bio.Ndb has been deprecated as the NDB website it used to parse has\
 been redesigned.',
  <type 'exceptions.DeprecationWarning'>,
  24): True}