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- Expansion.EdgeExpansion(Expansion.Expansion)
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- PianaEdgeExpansion
- Expansion.NodeExpansion(Expansion.Expansion)
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- PianaNodeExpansion
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- ExpansionSameCog
- ExpansionSameEC
- ExpansionSameInterpro
- ExpansionSameScop
class ExpansionSameCog(PianaNodeExpansion) |
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This class is used to propagate interactions from protein A to protein B if protein A and protein B share the same COG code
methods have the same name (to make trasparent kind of expansion) but are different from other expansions to use COG as expansion characteristic |
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- Method resolution order:
- ExpansionSameCog
- PianaNodeExpansion
- Expansion.NodeExpansion
- Expansion.Expansion
Methods defined here:
- __init__(self, piana_access_object, use_self_ints='yes', list_source_dbs='all', inverse_dbs='no', list_source_methods='all', inverse_methods='no')
- get_partners_of_nodes_sharing_characteristic(self, node_id)
- Returns a list of partner proteins of proteins that share cog with proteinPiana node_id
returns empty list if nothing found
ATTENTION: currently not being used!!!
- get_sharing_nodes(self, node_id)
- returns a list of nodes that share cog with node_id (node_id == proteinPiana in PianaGraph networks)
returns empty list if nothing found
Methods inherited from PianaNodeExpansion:
- class_test(self, node_id=None, class_name=None)
- tests whether the node_id belongs to class_name or not
returns 1 if class test is passed, 0 otherwise
In Piana this means, testing if proteinPiana node_id is of tax_id 'class_name'
'class_name' must be an integer (unless it is set to 'all')
- create_new_edge_attribute(self, edge_db_id=None, expansion_type=None, propagated_from_node=None, propagated_from_edge_id=None, propagated_from_db_edge_id=None, extended_from_node=None)
- returns attribute of type PianaGraphEdgeAttribute with given characteristics
expansion_type, propagated_from_node, propagated_from_edge are mandatory when defining a propagation
expansion_type, extended_from_node are mandatory when defining an extension
if edge_db_id is not None, it means we are creating an attribute for a given interactionPiana. In propagations edge_db_id will be None
because propagated edges do not exist as such in the database. Extensions will have an edge_db_id
- create_new_node_attribute(self, node_id=None)
- returns an attribute of type PianaGraphNodeAttribute with given characteristics
- get_db_edge_ids_from_node(self, node_id)
- Returns a list of interactionPiana (which is the db_edge_id describing interactions between node_id and all its partners
returns empty list if nothing is found
- get_edges_attributes_from_node(self, node_id)
- Returns a list of PianaGraphEdgeAttribute objects describing interactions between node_id and all its partners
returns empty list if nothing was found
- get_expansion_name(self)
- returns the name of the expansion
- get_external_code(self, node_id=None, id_type=None, alternative_id_types=[])
- returns the external code for node_id, first trying with id_type and then with alternative_id_types
if no code of id_type is found, string returned with alternative id type will follow the format "type_of_code_found:protein_code_value"
- get_partner_ids(self, node_id)
- Returns a list of partners (proteinPiana) of node_id
returns empty list if nothing is found
- get_partner_node_id(self, db_edge_id=None, node_id=None)
- Returns the partner node (a protein) of "node_id" in pianaDB interaction described by PianaGraphEdgeAttribute edge_attribute
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class ExpansionSameEC(PianaNodeExpansion) |
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This class is used to propagate interactions from protein A to protein B if protein A and protein B share the same EC code
methods have the same name (to make trasparent kind of expansion) but are different from other expansions to use EC as expansion characteristic |
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- Method resolution order:
- ExpansionSameEC
- PianaNodeExpansion
- Expansion.NodeExpansion
- Expansion.Expansion
Methods defined here:
- __init__(self, piana_access_object, use_self_ints='yes', list_source_dbs='all', inverse_dbs='no', list_source_methods='all', inverse_methods='no')
- get_sharing_nodes(self, node_id)
- returns a list of nodes that share ec with node_id (node_id == proteinPiana in PianaGraph networks)
returns empty list if nothing found
Methods inherited from PianaNodeExpansion:
- class_test(self, node_id=None, class_name=None)
- tests whether the node_id belongs to class_name or not
returns 1 if class test is passed, 0 otherwise
In Piana this means, testing if proteinPiana node_id is of tax_id 'class_name'
'class_name' must be an integer (unless it is set to 'all')
- create_new_edge_attribute(self, edge_db_id=None, expansion_type=None, propagated_from_node=None, propagated_from_edge_id=None, propagated_from_db_edge_id=None, extended_from_node=None)
- returns attribute of type PianaGraphEdgeAttribute with given characteristics
expansion_type, propagated_from_node, propagated_from_edge are mandatory when defining a propagation
expansion_type, extended_from_node are mandatory when defining an extension
if edge_db_id is not None, it means we are creating an attribute for a given interactionPiana. In propagations edge_db_id will be None
because propagated edges do not exist as such in the database. Extensions will have an edge_db_id
- create_new_node_attribute(self, node_id=None)
- returns an attribute of type PianaGraphNodeAttribute with given characteristics
- get_db_edge_ids_from_node(self, node_id)
- Returns a list of interactionPiana (which is the db_edge_id describing interactions between node_id and all its partners
returns empty list if nothing is found
- get_edges_attributes_from_node(self, node_id)
- Returns a list of PianaGraphEdgeAttribute objects describing interactions between node_id and all its partners
returns empty list if nothing was found
- get_expansion_name(self)
- returns the name of the expansion
- get_external_code(self, node_id=None, id_type=None, alternative_id_types=[])
- returns the external code for node_id, first trying with id_type and then with alternative_id_types
if no code of id_type is found, string returned with alternative id type will follow the format "type_of_code_found:protein_code_value"
- get_partner_ids(self, node_id)
- Returns a list of partners (proteinPiana) of node_id
returns empty list if nothing is found
- get_partner_node_id(self, db_edge_id=None, node_id=None)
- Returns the partner node (a protein) of "node_id" in pianaDB interaction described by PianaGraphEdgeAttribute edge_attribute
Methods inherited from Expansion.NodeExpansion:
- get_partners_of_nodes_sharing_characteristic(self, node_id)
- Returns a list of partner proteins of proteins that share cog with proteinPiana node_id
returns empty list if nothing found
ATTENTION: currently not being used!!!
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class ExpansionSameInterpro(PianaNodeExpansion) |
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This class is used to propagate interactions from protein A to protein B if protein A and protein B share the same interpro code
methods have the same name (to make trasparent kind of expansion) but are different from other expansions to use interPro as expansion characteristic |
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- Method resolution order:
- ExpansionSameInterpro
- PianaNodeExpansion
- Expansion.NodeExpansion
- Expansion.Expansion
Methods defined here:
- __init__(self, piana_access_object, use_self_ints='yes', list_source_dbs='all', inverse_dbs='no', list_source_methods='all', inverse_methods='no')
- get_sharing_nodes(self, node_id)
- returns a list of nodes that share interpro code with node_id (node_id == proteinPiana in PianaGraph networks)
returns empty list if nothing found
Methods inherited from PianaNodeExpansion:
- class_test(self, node_id=None, class_name=None)
- tests whether the node_id belongs to class_name or not
returns 1 if class test is passed, 0 otherwise
In Piana this means, testing if proteinPiana node_id is of tax_id 'class_name'
'class_name' must be an integer (unless it is set to 'all')
- create_new_edge_attribute(self, edge_db_id=None, expansion_type=None, propagated_from_node=None, propagated_from_edge_id=None, propagated_from_db_edge_id=None, extended_from_node=None)
- returns attribute of type PianaGraphEdgeAttribute with given characteristics
expansion_type, propagated_from_node, propagated_from_edge are mandatory when defining a propagation
expansion_type, extended_from_node are mandatory when defining an extension
if edge_db_id is not None, it means we are creating an attribute for a given interactionPiana. In propagations edge_db_id will be None
because propagated edges do not exist as such in the database. Extensions will have an edge_db_id
- create_new_node_attribute(self, node_id=None)
- returns an attribute of type PianaGraphNodeAttribute with given characteristics
- get_db_edge_ids_from_node(self, node_id)
- Returns a list of interactionPiana (which is the db_edge_id describing interactions between node_id and all its partners
returns empty list if nothing is found
- get_edges_attributes_from_node(self, node_id)
- Returns a list of PianaGraphEdgeAttribute objects describing interactions between node_id and all its partners
returns empty list if nothing was found
- get_expansion_name(self)
- returns the name of the expansion
- get_external_code(self, node_id=None, id_type=None, alternative_id_types=[])
- returns the external code for node_id, first trying with id_type and then with alternative_id_types
if no code of id_type is found, string returned with alternative id type will follow the format "type_of_code_found:protein_code_value"
- get_partner_ids(self, node_id)
- Returns a list of partners (proteinPiana) of node_id
returns empty list if nothing is found
- get_partner_node_id(self, db_edge_id=None, node_id=None)
- Returns the partner node (a protein) of "node_id" in pianaDB interaction described by PianaGraphEdgeAttribute edge_attribute
Methods inherited from Expansion.NodeExpansion:
- get_partners_of_nodes_sharing_characteristic(self, node_id)
- Returns a list of partner proteins of proteins that share cog with proteinPiana node_id
returns empty list if nothing found
ATTENTION: currently not being used!!!
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class ExpansionSameScop(PianaNodeExpansion) |
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This class is used to propagate interactions from protein A to protein B if protein A and protein B share the same SCOP family code
methods have the same name (to make trasparent kind of expansion) but are different from other expansions to use SCOP as expansion characteristic |
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- Method resolution order:
- ExpansionSameScop
- PianaNodeExpansion
- Expansion.NodeExpansion
- Expansion.Expansion
Methods defined here:
- __init__(self, piana_access_object, use_self_ints='yes', list_source_dbs='all', inverse_dbs='no', list_source_methods='all', inverse_methods='no')
- get_sharing_nodes(self, node_id)
- returns a list of nodes that share scop family code with node_id (node_id == proteinPiana in PianaGraph networks)
returns empty list if nothing found
Methods inherited from PianaNodeExpansion:
- class_test(self, node_id=None, class_name=None)
- tests whether the node_id belongs to class_name or not
returns 1 if class test is passed, 0 otherwise
In Piana this means, testing if proteinPiana node_id is of tax_id 'class_name'
'class_name' must be an integer (unless it is set to 'all')
- create_new_edge_attribute(self, edge_db_id=None, expansion_type=None, propagated_from_node=None, propagated_from_edge_id=None, propagated_from_db_edge_id=None, extended_from_node=None)
- returns attribute of type PianaGraphEdgeAttribute with given characteristics
expansion_type, propagated_from_node, propagated_from_edge are mandatory when defining a propagation
expansion_type, extended_from_node are mandatory when defining an extension
if edge_db_id is not None, it means we are creating an attribute for a given interactionPiana. In propagations edge_db_id will be None
because propagated edges do not exist as such in the database. Extensions will have an edge_db_id
- create_new_node_attribute(self, node_id=None)
- returns an attribute of type PianaGraphNodeAttribute with given characteristics
- get_db_edge_ids_from_node(self, node_id)
- Returns a list of interactionPiana (which is the db_edge_id describing interactions between node_id and all its partners
returns empty list if nothing is found
- get_edges_attributes_from_node(self, node_id)
- Returns a list of PianaGraphEdgeAttribute objects describing interactions between node_id and all its partners
returns empty list if nothing was found
- get_expansion_name(self)
- returns the name of the expansion
- get_external_code(self, node_id=None, id_type=None, alternative_id_types=[])
- returns the external code for node_id, first trying with id_type and then with alternative_id_types
if no code of id_type is found, string returned with alternative id type will follow the format "type_of_code_found:protein_code_value"
- get_partner_ids(self, node_id)
- Returns a list of partners (proteinPiana) of node_id
returns empty list if nothing is found
- get_partner_node_id(self, db_edge_id=None, node_id=None)
- Returns the partner node (a protein) of "node_id" in pianaDB interaction described by PianaGraphEdgeAttribute edge_attribute
Methods inherited from Expansion.NodeExpansion:
- get_partners_of_nodes_sharing_characteristic(self, node_id)
- Returns a list of partner proteins of proteins that share cog with proteinPiana node_id
returns empty list if nothing found
ATTENTION: currently not being used!!!
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class PianaNodeExpansion(Expansion.NodeExpansion) |
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Class that contains methods used for all kinds of Piana Node expansions
Specific piana expansions only need to implement the methods that return a list of nodes that share a node characteristic (method get_expanded_nodes() )
This is the class used for Node Expansions: propagating interactions of one node to another |
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- Method resolution order:
- PianaNodeExpansion
- Expansion.NodeExpansion
- Expansion.Expansion
Methods defined here:
- __init__(self, piana_access_object=None, name='', use_self_ints='yes', list_source_dbs='all', inverse_dbs='no', list_source_methods='all', inverse_methods='no')
- class_test(self, node_id=None, class_name=None)
- tests whether the node_id belongs to class_name or not
returns 1 if class test is passed, 0 otherwise
In Piana this means, testing if proteinPiana node_id is of tax_id 'class_name'
'class_name' must be an integer (unless it is set to 'all')
- create_new_edge_attribute(self, edge_db_id=None, expansion_type=None, propagated_from_node=None, propagated_from_edge_id=None, propagated_from_db_edge_id=None, extended_from_node=None)
- returns attribute of type PianaGraphEdgeAttribute with given characteristics
expansion_type, propagated_from_node, propagated_from_edge are mandatory when defining a propagation
expansion_type, extended_from_node are mandatory when defining an extension
if edge_db_id is not None, it means we are creating an attribute for a given interactionPiana. In propagations edge_db_id will be None
because propagated edges do not exist as such in the database. Extensions will have an edge_db_id
- create_new_node_attribute(self, node_id=None)
- returns an attribute of type PianaGraphNodeAttribute with given characteristics
- get_db_edge_ids_from_node(self, node_id)
- Returns a list of interactionPiana (which is the db_edge_id describing interactions between node_id and all its partners
returns empty list if nothing is found
- get_edges_attributes_from_node(self, node_id)
- Returns a list of PianaGraphEdgeAttribute objects describing interactions between node_id and all its partners
returns empty list if nothing was found
- get_expansion_name(self)
- returns the name of the expansion
- get_external_code(self, node_id=None, id_type=None, alternative_id_types=[])
- returns the external code for node_id, first trying with id_type and then with alternative_id_types
if no code of id_type is found, string returned with alternative id type will follow the format "type_of_code_found:protein_code_value"
- get_partner_ids(self, node_id)
- Returns a list of partners (proteinPiana) of node_id
returns empty list if nothing is found
- get_partner_node_id(self, db_edge_id=None, node_id=None)
- Returns the partner node (a protein) of "node_id" in pianaDB interaction described by PianaGraphEdgeAttribute edge_attribute
Methods inherited from Expansion.NodeExpansion:
- get_partners_of_nodes_sharing_characteristic(self, node_id)
- Returns a list of partner proteins of proteins that share cog with proteinPiana node_id
returns empty list if nothing found
ATTENTION: currently not being used!!!
- get_sharing_nodes(self, node_id)
- This must be overridden with a method that returns a list of nodes that share a characteristic with node_id
This characteristic will determine the expansion: edges will be propagated between nodes that share that characteristic.
This method is the only one that is specific to this characteristic: all the other methods that have to be overridden
are specific to the external database, but not to the characteristic
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