Package biana :: Package BianaParser :: Module ncbiGenPeptParser :: Class NcbiGenPeptParserGenpeptParser
[hide private]
[frames] | no frames]

Class NcbiGenPeptParserGenpeptParser

source code


Genpept Parser class

Instance Methods [hide private]
 
__init__(self)
Starts the bianaParser Object
source code
 
parse_database(self)
Method to be overwritten by specific parsers
source code
 
parse_fasta_file(self, fasta_file_fd) source code
 
parse_genpept_entry(self, header_line, sequence) source code

Inherited from bianaParser.BianaParser: add_to_log, close, get_log_string, initialize_input_file_descriptor, parseArguments, print_help, start

Inherited from bianaParser.BianaParser (private): _indent, _splitsize

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

Class Variables [hide private]
  name = 'ncbi_genpept'
  description = 'Inserts NCBI Genpet database into BIANA'
  external_entity_definition = 'A external entity represents a p...
  external_entity_relations = ''
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

source code 

Starts the bianaParser Object

Overrides: object.__init__
(inherited documentation)

parse_database(self)

source code 

Method to be overwritten by specific parsers

The method must include the calls to control lock and unlock database procedures

Overrides: bianaParser.BianaParser.parse_database
(inherited documentation)

Class Variable Details [hide private]

external_entity_definition

Value:
'A external entity represents a protein'