Package biana :: Module biana_globals

Module biana_globals

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

Variables

[hide private]

DBNAME = 'biana'

DBUSER = 'root'

DBPASS = 'root'

DBHOST = 'localhost'

DBPORT = None

DBSOCKET = '/home/jgarcia/local/mysql/var/mysql.sock'

EXTERNAL_ENTITY_TYPES = ['protein', 'DNA', 'RNA', 'mRNA', 'tRN...

EXTERNAL_ENTITY_RELATION_TYPES = ['interaction', 'no_interacti...

EXTERNAL_ENTITY_IDENTIFIER_ATTRIBUTES = [('CHEBI', 'integer un...

EXTERNAL_ENTITY_GENERAL_ATTRIBUTES = []

PROMISCUOUS_EXTERNAL_ENTITY_TYPES_DICT = [('SCOPElement', 'PDB')]

VALID_IDENTIFIER_REFERENCE_TYPES = ['unique', 'previous', 'ali...

CROSSABLE_ATTRIBUTES = Set(['uniprotaccession', 'sequence', 'i...

EXTERNAL_ENTITY_VERSIONABLE_IDENTIFIER_ATTRIBUTE_TYPES = [('Ac...

EXTERNAL_ENTITY_DESCRIPTIVE_SEARCHABLE_ATTRIBUTE_TYPES = [('Di...

EXTERNAL_ENTITY_DESCRIPTIVE_ATTRIBUTE_TYPES = [('Pubmed', 'int...

EXTERNAL_ENTITY_NUMERIC_ATTRIBUTE_TYPES = [('Pvalue', 'double'...

EXTERNAL_ENTITY_SPECIAL_ATTRIBUTE_TYPES = {'NucleotideSequence...

EXTERNAL_ENTITY_RELATION_PARTICIPANT_ATTRIBUTE_TYPES = [('card...

CLUSTALW_EXEC = '/usr/local/bin/clustalw'

FORMATDB_EXEC = '/soft/bio/sequence/blast-2.2.17/bin/formatdb'

BLASTALL_EXEC = '/soft/bio/sequence/blast-2.2.17/bin/blastall'

BL2SEQ_EXEC = '/soft/bio/sequence/blast-2.2.17/bin/bl2seq'

TCOFFEE_EXEC = '/Users/javigx2/phD/external_software/tcoffee/T...

DSSP_EXEC = '/soft/bio/structure/dssp/dsspcmbi'

CD_HIT_PATH = '/home/jgarcia/programs/CD-HIT/cd-hit/'

TEMPORAL_PATH = None

Variables Details

[hide private]

EXTERNAL_ENTITY_TYPES

Value:

['protein',
 'DNA',
 'RNA',
 'mRNA',
 'tRNA',
 'rRNA',
 'CDS',
 'gene',
...

EXTERNAL_ENTITY_RELATION_TYPES

Value:

['interaction',
 'no_interaction',
 'reaction',
 'functional_association',
 'cluster',
 'homology',
 'pathway',
 'alignment',
...

EXTERNAL_ENTITY_IDENTIFIER_ATTRIBUTES

Value:

[('CHEBI', 'integer unsigned'),
 ('COG', 'varchar(10)'),
 ('CYGD', 'varchar(15)'),
 ('DIP', 'varchar(6)'),
 ('EC', 'varchar(30)'),
 ('Encode', 'varchar(14)'),
 ('Ensembl', 'varchar(40)'),
 ('FlyBase', 'varchar(13)'),
...

VALID_IDENTIFIER_REFERENCE_TYPES

Value:

['unique',
 'previous',
 'alias',
 'cross-reference',
 'synonym',
 'short-name',
 'exact_synonym',
 'related_synonym']

CROSSABLE_ATTRIBUTES

Value:

Set(['uniprotaccession', 'sequence', 'ipi', 'taxid', 'ec', 'uniprotent
ry', 'genesymbol', 'refseq', 'geneid'])

EXTERNAL_ENTITY_VERSIONABLE_IDENTIFIER_ATTRIBUTE_TYPES

Value:

[('AccessionNumber', 'varchar(15)'),
 ('RefSeq', 'varchar(15)'),
 ('TIGR', 'varchar(255)'),
 ('UniprotAccession', 'varchar(9)')]

EXTERNAL_ENTITY_DESCRIPTIVE_SEARCHABLE_ATTRIBUTE_TYPES

Value:

[('Disease', 'text(2000)'),
 ('Function', 'text'),
 ('Keyword', 'varchar(50)'),
 ('Description', 'text'),
 ('SubcellularLocation', 'text(400)'),
 ('Name', 'varchar(255)')]

EXTERNAL_ENTITY_DESCRIPTIVE_ATTRIBUTE_TYPES

Value:

[('Pubmed', 'integer(3) unsigned'), ('Formula', 'varchar(255)')]

EXTERNAL_ENTITY_NUMERIC_ATTRIBUTE_TYPES

Value:

[('Pvalue', 'double'), ('Score', 'double')]

EXTERNAL_ENTITY_SPECIAL_ATTRIBUTE_TYPES

Value:

{'NucleotideSequence': {'fields': [('value', 'binary(16)'),
                                   ('sequenceType',
                                    'ENUM("dna","rna")',
                                    False)],
                        'indices': ('value')},
 'PDB': {'fields': [('value', 'char(4)'),
                    ('chain', 'varchar(4)', True),
                    ('pdb_range', 'varchar(255)', True)],
...

EXTERNAL_ENTITY_RELATION_PARTICIPANT_ATTRIBUTE_TYPES

Value:

[('cardinality', 'smallint unsigned'),
 ('detection_method', 'smallint unsigned'),
 ('GO', 'integer(3) unsigned'),
 ('KeggCode', 'varchar(6)'),
 ('role',
  'ENUM("batch","product","substrate","catalyst","prey","bait","neutra
l","acceptor","donor","self","ancillary","enzyme","enzyme target","inh
ibitor","cofactor","stimulator","activates","inhibits","allosteric_inh
...

TCOFFEE_EXEC

Value:

'/Users/javigx2/phD/external_software/tcoffee/T-COFFEE_distribution_Ve
rsion_7.04/bin/macosx/t_coffee'