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

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Class STRINGParser

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STRING Parser Class

Instance Methods

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__init__(self)
Starts the bianaParser Object

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parse_database(self)
Method that implements the specific operations of string parser

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check_time(self)

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_readGivenNumberOfSequencesToDictionary(self, sequences_file_fd, lineLastRed, nSequence)

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_readNextSequenceInformationFromSequenceFile(self, sequences_file_fd, line)

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_insert_new_string_protein_object_into_database(self, id_word, sequence, list_information_tuple)

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_insert_protein_information_from_alias_file_to_database(self, aliases_file)

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_fetch_given_list_protein_information_from_database(self, list_id)

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_fetch_given_protein_information_from_database(self, id_word)

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_remove_protein_information_from_database(self)

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_get_data_file_names(self)

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_get_file_descriptor(self, file)

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_close_file_descriptor(self, fd)

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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

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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

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Inherited from object: __class__

Method Details

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init(self)
(Constructor)

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Starts the bianaParser Object

Overrides: object.__init__: (inherited documentation)

parse_database(self)

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Method that implements the specific operations of string parser

Overrides: bianaParser.BianaParser.parse_database

Class Variable Details

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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,
...

Class STRINGParser

__init__(self) (Constructor)

parse_database(self)

description

external_entity_relations

datatype_to_biana_type

init(self)
(Constructor)