Module database2biana

source code

Functions

[hide private]

run()
Runs the script to insert the parser to the database

source code

get_available_parsers_info()
Returns a list of tuples with the information of the parsers.

source code

Variables

[hide private]

site_packages_path = None

biana_path = '/home/jgarcia/phD_project/BIANA_PROJECT/biana/bi...

list_all_files = ['stringParser.py.~1.20.~', 'control_ncbi_gen...

not_allowed_import_files = ['bianaParser.py', 'database2biana....

list_python_files = ['david_sequences_parser.py', 'keggligandP...

parserObjects = {'biopax_level_2': <class 'biopaxLevel2Parser....

imports = [<module 'david_sequences_parser' from '/home/jgarci...

current_dir = 'gnomecanvas.so'

current_file = 'GenericParser.py'

current_path_index = 26

x = 'GenericParser.py'

Function Details

[hide private]

get_available_parsers_info()

source code

Returns a list of tuples with the information of the parsers. (parser_name, parser_description, external_entity_definition)

Variables Details

[hide private]

biana_path

Value:

'/home/jgarcia/phD_project/BIANA_PROJECT/biana/biana/src/biana/BianaPa
rser'

list_all_files

Value:

['stringParser.py.~1.20.~',
 'control_ncbi_genpept.nohup',
 'keggligandParser.py.~1.7.~',
 'david_sequences_parser.py',
 'psimioboParser.py.~1.10.~',
 'keggligandParser.py',
 'pfamParser.py.~1.8.~',
 'pdbParser.pyc',
...

not_allowed_import_files

Value:

['bianaParser.py',
 'database2biana.py',
 '__init__.py',
 'psi_MiXMLParser.py']

list_python_files

Value:

['david_sequences_parser.py',
 'keggligandParser.py',
 'pfamParser.py',
 'stringParser.py',
 'scopParser.py',
 'keggGeneParser.py',
 'ncbiGenPeptParser.py',
 'keggKOParser.py',
...

parserObjects

Value:

{'biopax_level_2': <class 'biopaxLevel2Parser.BiopaxLevel2Parser'>,
 'cog': <class 'cogParser.CogParser'>,
 'david_human_sequences': <class 'david_sequences_parser.DavidSequence
sParser'>,
 'david_human_sequences_nr': <class 'david_sequences_nr_parser.DavidSe
quencesParserNr'>,
 'david_parser': <class 'DavidParser.DavidParser'>,
 'generic': <class 'GenericParser.GenericParser'>,
...

imports

Value:

[<module 'david_sequences_parser' from '/home/jgarcia/phD_project/BIAN
A_PROJECT/biana/biana/src/biana/BianaParser/david_sequences_parser.pyc
'>,
 <module 'keggligandParser' from '/home/jgarcia/phD_project/BIANA_PROJ
ECT/biana/biana/src/biana/BianaParser/keggligandParser.pyc'>,
 <module 'pfamParser' from '/home/jgarcia/phD_project/BIANA_PROJECT/bi
ana/biana/src/biana/BianaParser/pfamParser.pyc'>,
 <module 'stringParser' from '/home/jgarcia/phD_project/BIANA_PROJECT/
...