Package biana :: Package BianaParser :: Module stringParser :: Class STRINGParser
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Class STRINGParser

source code


STRING Parser Class

Instance Methods [hide private]
 
__init__(self)
Starts the bianaParser Object
source code
 
parse_database(self)
Method that implements the specific operations of string parser
source code
 
check_time(self) source code
 
_readGivenNumberOfSequencesToDictionary(self, sequences_file_fd, lineLastRed, nSequence) source code
 
_readNextSequenceInformationFromSequenceFile(self, sequences_file_fd, line) source code
 
_insert_new_string_protein_object_into_database(self, id_word, sequence, list_information_tuple) source code
 
_insert_protein_information_from_alias_file_to_database(self, aliases_file) source code
 
_fetch_given_list_protein_information_from_database(self, list_id) source code
 
_fetch_given_protein_information_from_database(self, id_word) source code
 
_remove_protein_information_from_database(self) source code
 
_get_data_file_names(self) source code
 
_get_file_descriptor(self, file) source code
 
_close_file_descriptor(self, fd) 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]
  N_MAX_ENTRY_AT_ONCE = 5000
  name = 'string'
  description = 'This program fills up tables in database biana ...
  external_entity_definition = 'A protein in STRING with sequence'
  external_entity_relations = 'A link given between two proteins...
  datatype_to_biana_type = {'AFFY_C_elegans': None, 'AFFY_Canine...
  swissprot_re = re.compile(r'SWISSPROT_[A-Z]{2}\.*')
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 that implements the specific operations of string parser

Overrides: bianaParser.BianaParser.parse_database

Class Variable Details [hide private]

description

Value:
'This program fills up tables in database biana related with STRING'

external_entity_relations

Value:
'A link given between two proteins in STRING with score'

datatype_to_biana_type

Value:
{'AFFY_C_elegans': None,
 'AFFY_Canine': None,
 'AFFY_Chicken': None,
 'AFFY_DrosGenome1': None,
 'AFFY_Drosophila_2': None,
 'AFFY_HC_G110': None,
 'AFFY_HC_G110 and CCDS': None,
 'AFFY_HG_Focus': None,
...