def get_intersection_of_3_set():
from biana.biana_commands import administration, available_sessions, create_new_session
from biana.BianaObjects import BianaSessionManager
import biana.utilities.identifier_utilities as id_utils
create_new_session(sessionID="biana_session",dbname=DB_NAME, dbhost=DB_HOST, dbuser=DB_USER, dbpassword=DB_PASS, unification_protocol=UNIFICATION_PROTOCOL)
objSession = available_sessions["biana_session"]
objSession.create_new_user_entity_set( identifier_description_list = id_utils.read_identifier_list_from_file(BONE_FILE, id_type="uniprotaccession"), external_entity_attribute_restriction_list=[("taxid","9606")], id_type="embedded",new_user_entity_set_id="bone")
objSession.create_new_user_entity_set( identifier_description_list = id_utils.read_identifier_list_from_file(LIVER_FILE, id_type="uniprotaccession"), external_entity_attribute_restriction_list=[("taxid","9606")], id_type="embedded",new_user_entity_set_id="liver")
objSession.create_new_user_entity_set( identifier_description_list = id_utils.read_identifier_list_from_file(LUNG_FILE, id_type="uniprotaccession"), external_entity_attribute_restriction_list=[("taxid","9606")], id_type="embedded",new_user_entity_set_id="lung")
print "Bone - Liver - Lung User Entity Sets are created..", objSession
objSession.create_network( user_entity_set_id = "bone" , level = 1 , relation_type_list=["complex","interaction","pathway","reaction"] , include_relations_last_level = True , use_self_relations = False)
objSession.create_network( user_entity_set_id = "liver" , level = 1 , relation_type_list=["complex","interaction","pathway","reaction"] , include_relations_last_level = True , use_self_relations = False)
objSession.create_network( user_entity_set_id = "lung" , level = 1 , relation_type_list=["complex","interaction","pathway","reaction"] , include_relations_last_level = True , use_self_relations = False)
print "Bone - Liver - Lung Networks are created..", objSession
objSession.get_intersection_of_user_entity_set_list([objSession.get_user_entity_set("bone"), objSession.get_user_entity_set("liver"), objSession.get_user_entity_set("lung")], include_relations=True, new_user_entity_set_id="intersection")
objSession.get_intersection_of_user_entity_set_list([objSession.get_user_entity_set("bone"), objSession.get_user_entity_set("liver")], include_relations=True, new_user_entity_set_id="bone_liver")
objSession.get_intersection_of_user_entity_set_list([objSession.get_user_entity_set("bone"), objSession.get_user_entity_set("lung")], include_relations=True, new_user_entity_set_id="bone_lung")
objSession.get_intersection_of_user_entity_set_list([objSession.get_user_entity_set("liver"), objSession.get_user_entity_set("lung")], include_relations=True, new_user_entity_set_id="liver_lung")
print "Intersections are created..", objSession
return
def get_seed_connected_nodes():
from biana.biana_commands import administration, available_sessions, create_new_session
from biana.BianaObjects import BianaSessionManager
import sets
import biana.utilities.identifier_utilities as id_utils
t_init = time.clock()
relation_type_list = ["interaction"] # ["reaction","complex","pathway","interaction"]
# Create a new BIANA session
create_new_session(sessionID="biana_session",dbname=DB_NAME, dbhost=DB_HOST, dbuser=DB_USER, dbpassword=DB_PASS, unification_protocol=UNIFICATION_PROTOCOL)
objSession = available_sessions["biana_session"]
#identifier_description_list = id_utils.read_identifier_list_from_file("/home/emre/arastirma/colloboration/seeds_intracranial_and_aneurysm_and_mesh_genetics.txt", "genesymbol")
identifier_description_list = id_utils.read_identifier_list_from_file("/home/emre/arastirma/colloboration/subarachnoid_and_hemorrhage_or_haemorrhage_and_mesh_genetics.seeds", "genesymbol")
# Create a new User Entity Set (group of biomolecules) in this session
uESet1 = objSession.create_new_user_entity_set( identifier_description_list = identifier_description_list, external_entity_attribute_restriction_list=[("taxid","9606")], id_type="embedded", new_user_entity_set_id="User_Entity_Set_1")
t_1 = time.clock()
# Get relations of biomolecules in this set
objSession.create_network( user_entity_set_id = "User_Entity_Set_1" , level = 1, relation_type_list= relation_type_list, include_relations_last_level = False, use_self_relations = False)
t_2 = time.clock()
print "t_network:", t_2-t_1
# Select seeds and nodes connected by seeds in the network of this User Entity Set
user_entities_to_print = sets.Set(uESet1.get_user_entity_ids(level=0))|uESet1.get_user_entity_ids_by_linker_degree_cutoff(2)
objSession.select_user_entities_from_user_entity_set("User_Entity_Set_1", user_entities_to_print, clear_previous_selection=True)
objSession.tag_selected_user_entities(user_entity_set_id="User_Entity_Set_1", tag="seed+connected")
t_3 = time.clock()
print "t_connected:", t_3-t_2
# Output set details - only selected nodes
#objSession.output_user_entity_set_details(user_entity_set_id = "User_Entity_Set_1", out_method = open("nodes_selected.out", "w").write, attributes=["genesymbol", "uniprotaccession", "hgnc"], include_level_info=True, include_degree_info=True, level=None, only_selected=True, output_format="tabulated", include_tags_info = True, include_tags_linkage_degree_info=[], substitute_node_attribute_if_not_exists=True, output_1_value_per_attribute=False, include_command_in_rows=False)
# Output set details - all nodes
objSession.output_user_entity_set_details(user_entity_set_id = "User_Entity_Set_1", out_method = open("nodes.out", "w").write, attributes=["genesymbol", "uniprotaccession", "hgnc"], include_level_info=True, include_degree_info=True, level=None, only_selected=False, output_format="tabulated", include_tags_info = True, include_tags_linkage_degree_info=[], substitute_node_attribute_if_not_exists=True, output_1_value_per_attribute=False, include_command_in_rows=False)
t_4 = time.clock()
print "t_nodes:", t_4-t_3
# Output network details
objSession.output_user_entity_set_network(user_entity_set_id = "User_Entity_Set_1", out_method=open("network.out", "w").write, node_attributes = [], participant_attributes = [], relation_attributes=["Method_id"], allowed_relation_types="all", include_relation_ids=False, include_participant_ids=True, include_relation_type=True, include_relation_sources=True, output_1_value_per_attribute=False, output_format="tabulated", only_selected=False, substitute_node_attribute_if_not_exists=True, include_participant_tags=False, include_relation_tags = False, include_unconnected_nodes=False)
t_5 = time.clock()
print "t_network:", t_5-t_4
def get_intersection_of_3_set():
from biana.biana_commands import administration, available_sessions, create_new_session
from biana.BianaObjects import BianaSessionManager
import biana.utilities.identifier_utilities as id_utils
create_new_session(sessionID="biana_session",
dbname=DB_NAME,
dbhost=DB_HOST,
dbuser=DB_USER,
dbpassword=DB_PASS,
unification_protocol=UNIFICATION_PROTOCOL)
objSession = available_sessions["biana_session"]
objSession.create_new_user_entity_set(
identifier_description_list=id_utils.read_identifier_list_from_file(
BONE_FILE, id_type="uniprotaccession"),
external_entity_attribute_restriction_list=[("taxid", "9606")],
id_type="embedded",
new_user_entity_set_id="bone")
objSession.create_new_user_entity_set(
identifier_description_list=id_utils.read_identifier_list_from_file(
LIVER_FILE, id_type="uniprotaccession"),
external_entity_attribute_restriction_list=[("taxid", "9606")],
id_type="embedded",
new_user_entity_set_id="liver")
objSession.create_new_user_entity_set(
identifier_description_list=id_utils.read_identifier_list_from_file(
LUNG_FILE, id_type="uniprotaccession"),
external_entity_attribute_restriction_list=[("taxid", "9606")],
id_type="embedded",
new_user_entity_set_id="lung")
print "Bone - Liver - Lung User Entity Sets are created..", objSession
objSession.create_network(
user_entity_set_id="bone",
level=1,
relation_type_list=["complex", "interaction", "pathway", "reaction"],
include_relations_last_level=True,
use_self_relations=False)
objSession.create_network(
user_entity_set_id="liver",
level=1,
relation_type_list=["complex", "interaction", "pathway", "reaction"],
include_relations_last_level=True,
use_self_relations=False)
objSession.create_network(
user_entity_set_id="lung",
level=1,
relation_type_list=["complex", "interaction", "pathway", "reaction"],
include_relations_last_level=True,
use_self_relations=False)
print "Bone - Liver - Lung Networks are created..", objSession
objSession.get_intersection_of_user_entity_set_list(
[
objSession.get_user_entity_set("bone"),
objSession.get_user_entity_set("liver"),
objSession.get_user_entity_set("lung")
],
include_relations=True,
new_user_entity_set_id="intersection")
objSession.get_intersection_of_user_entity_set_list(
[
objSession.get_user_entity_set("bone"),
objSession.get_user_entity_set("liver")
],
include_relations=True,
new_user_entity_set_id="bone_liver")
objSession.get_intersection_of_user_entity_set_list(
[
objSession.get_user_entity_set("bone"),
objSession.get_user_entity_set("lung")
],
include_relations=True,
new_user_entity_set_id="bone_lung")
objSession.get_intersection_of_user_entity_set_list(
[
objSession.get_user_entity_set("liver"),
objSession.get_user_entity_set("lung")
],
include_relations=True,
new_user_entity_set_id="liver_lung")
print "Intersections are created..", objSession
return
def get_seed_connected_nodes():
from biana.biana_commands import administration, available_sessions, create_new_session
from biana.BianaObjects import BianaSessionManager
import sets
import biana.utilities.identifier_utilities as id_utils
t_init = time.clock()
relation_type_list = ["interaction"
] # ["reaction","complex","pathway","interaction"]
# Create a new BIANA session
create_new_session(sessionID="biana_session",
dbname=DB_NAME,
dbhost=DB_HOST,
dbuser=DB_USER,
dbpassword=DB_PASS,
unification_protocol=UNIFICATION_PROTOCOL)
objSession = available_sessions["biana_session"]
#identifier_description_list = id_utils.read_identifier_list_from_file("/home/emre/arastirma/colloboration/seeds_intracranial_and_aneurysm_and_mesh_genetics.txt", "genesymbol")
identifier_description_list = id_utils.read_identifier_list_from_file(
"/home/emre/arastirma/colloboration/subarachnoid_and_hemorrhage_or_haemorrhage_and_mesh_genetics.seeds",
"genesymbol")
# Create a new User Entity Set (group of biomolecules) in this session
uESet1 = objSession.create_new_user_entity_set(
identifier_description_list=identifier_description_list,
external_entity_attribute_restriction_list=[("taxid", "9606")],
id_type="embedded",
new_user_entity_set_id="User_Entity_Set_1")
t_1 = time.clock()
# Get relations of biomolecules in this set
objSession.create_network(user_entity_set_id="User_Entity_Set_1",
level=1,
relation_type_list=relation_type_list,
include_relations_last_level=False,
use_self_relations=False)
t_2 = time.clock()
print "t_network:", t_2 - t_1
# Select seeds and nodes connected by seeds in the network of this User Entity Set
user_entities_to_print = sets.Set(uESet1.get_user_entity_ids(
level=0)) | uESet1.get_user_entity_ids_by_linker_degree_cutoff(2)
objSession.select_user_entities_from_user_entity_set(
"User_Entity_Set_1",
user_entities_to_print,
clear_previous_selection=True)
objSession.tag_selected_user_entities(
user_entity_set_id="User_Entity_Set_1", tag="seed+connected")
t_3 = time.clock()
print "t_connected:", t_3 - t_2
# Output set details - only selected nodes
#objSession.output_user_entity_set_details(user_entity_set_id = "User_Entity_Set_1", out_method = open("nodes_selected.out", "w").write, attributes=["genesymbol", "uniprotaccession", "hgnc"], include_level_info=True, include_degree_info=True, level=None, only_selected=True, output_format="tabulated", include_tags_info = True, include_tags_linkage_degree_info=[], substitute_node_attribute_if_not_exists=True, output_1_value_per_attribute=False, include_command_in_rows=False)
# Output set details - all nodes
objSession.output_user_entity_set_details(
user_entity_set_id="User_Entity_Set_1",
out_method=open("nodes.out", "w").write,
attributes=["genesymbol", "uniprotaccession", "hgnc"],
include_level_info=True,
include_degree_info=True,
level=None,
only_selected=False,
output_format="tabulated",
include_tags_info=True,
include_tags_linkage_degree_info=[],
substitute_node_attribute_if_not_exists=True,
output_1_value_per_attribute=False,
include_command_in_rows=False)
t_4 = time.clock()
print "t_nodes:", t_4 - t_3
# Output network details
objSession.output_user_entity_set_network(
user_entity_set_id="User_Entity_Set_1",
out_method=open("network.out", "w").write,
node_attributes=[],
participant_attributes=[],
relation_attributes=["Method_id"],
allowed_relation_types="all",
include_relation_ids=False,
include_participant_ids=True,
include_relation_type=True,
include_relation_sources=True,
output_1_value_per_attribute=False,
output_format="tabulated",
only_selected=False,
substitute_node_attribute_if_not_exists=True,
include_participant_tags=False,
include_relation_tags=False,
include_unconnected_nodes=False)
t_5 = time.clock()
print "t_network:", t_5 - t_4
