def create_input_transition_nodes(cursor, starting_species_list, operon_id, input_transition_id_dict):
"""Create input transition nodes list from the corresponding operon_id.
Argument(s):
cursor - sqlite3 cursor object
starting_species_list - a list of species activating an operon
operon_id - sbider based operon id
input_transition_id_dict - dictionary mapping input transitions to corresponding species
Return:
A tuple of input transition nodes list (with abbreviation) and
input transition id list.
For example:
( [ ("ope_1-1", "pLux-->gfp", "sbol_image_path_1"), ("ope_2-1", "pLambda-->gfp", "sbol_image_path_2"), ... ],
["1-1", "2-1", ...] )
"""
activated_it_ids = determine_operon_activated_input_transition(cursor, starting_species_list, operon_id,
input_transition_id_dict)
it_node_abbrev_list = []
activated_it_id_list = []
for activated_it_id in activated_it_ids:
it_node = db.db_select(cursor, "InputTransition", "*", ["it_id"], ["="], [activated_it_id], [""])
it_node = list(it_node.fetchone())
it_node_abbrev = add_node_id_abbreviation(it_node, "it_", 0)
it_node_abbrev_list.append(it_node_abbrev)
activated_it_id_list.append(activated_it_id)
return it_node_abbrev_list, activated_it_id_list
def get_node1_list_from_node2_id(cursor, node1_node2_relationship_table,
node2_id, node2_id_type, node1_table_name,
node1_id_type):
"""Query the database to find all node1's from node2's id.
It's possible to have multiple node1's map to node2.
Argument(s):
cursor - sqlite3 cursor object
node1_node2_relationship_table - table_name relating node1 and node2
node2_id - string representation of node1_id
node2_id_type - node2_id type being used in the sbider database
node1_table_name - table_name where node information exists
node1_id_type - node1_id type being used in the sbider database
Return:
A list of nodes representing all node1's related to node2.
"""
node_id = db.db_select(cursor, node1_node2_relationship_table,
[node1_id_type], [node2_id_type], ["="],
["'" + node2_id + "'"], [""])
node_id_list = node_id.fetchall()
node_id_list = list_of_lists(node_id_list)
node_list = []
for node_info in node_id_list:
node_ = get_node_from_id(cursor, node1_table_name, node_info[0],
node1_id_type)
node_ = list(node_)
node_list.append(node_)
return node_list
def get_node_list_from_other_node_id(cursor, node_other_node_relationship_table, other_node_id, other_node_id_type,
node_table_name, node_id_type):
node_id = db.db_select(cursor, node_other_node_relationship_table,
[node_id_type],
[other_node_id_type],
["="],
["'" + other_node_id + "'"],
[""])
#print "node_id:", node_id
node_id_list = node_id.fetchall()
node_id_list = list_of_lists(node_id_list)
#print "node_id_list:", node_id_list
node_list = []
for node_id in node_id_list:
#print "node_id:", node_id
node = get_node_from_id(cursor, node_table_name, node_id[0], node_id_type)
#print "node:", node
node = list(node)
node_list.append(node)
return node_list
def get_node1_list_from_node2_id(cursor, node1_node2_relationship_table, node2_id, node2_id_type,
node1_table_name, node1_id_type):
"""Query the database to find all node1's from node2's id.
It's possible to have multiple node1's map to node2.
Argument(s):
cursor - sqlite3 cursor object
node1_node2_relationship_table - table_name relating node1 and node2
node2_id - string representation of node1_id
node2_id_type - node2_id type being used in the sbider database
node1_table_name - table_name where node information exists
node1_id_type - node1_id type being used in the sbider database
Return:
A list of nodes representing all node1's related to node2.
"""
node_id = db.db_select(cursor, node1_node2_relationship_table,
[node1_id_type],
[node2_id_type],
["="],
["'" + node2_id + "'"],
[""])
node_id_list = node_id.fetchall()
node_id_list = list_of_lists(node_id_list)
node_list = []
for node_info in node_id_list:
node_ = get_node_from_id(cursor, node1_table_name, node_info[0], node1_id_type)
node_ = list(node_)
node_list.append(node_)
return node_list
def determine_operon_activated_input_transition(cursor, starting_species_list, operon_id, input_transition_id_dict):
"""Determining which input transition is activating an operon.
Argument(s):
cursor - sqlite3 cursor object
starting_species_list - a list of species activating an operon
operon_id - sbider based operon id
id_id_dict - dictionary mapping input transitions to corresponding species
Return:
A list of transitions that activate the operon (from operon_id).
For example: ["it_1", "it_2", ...]
"""
starting_species_set = set(tuple(starting_species_list))
it_trans_id_list = db.db_select(cursor, "OperonInputTransition", ["it_id"], ["ope_id"], ["="],
["'" + operon_id + "'"], [""])
it_trans_id_list = it_trans_id_list.fetchall()
it_trans_id_list = list_of_lists(it_trans_id_list)
it_trans_id_list = merge_list_of_lists(it_trans_id_list)
activated_it_id_list = []
for it_trans_id in it_trans_id_list:
activating_species_set = set(input_transition_id_dict[it_trans_id])
if starting_species_set.issuperset(activating_species_set):
activated_it_id_list.append(it_trans_id)
return activated_it_id_list
def get_input_transition_species_dictionary(cursor):
"""
Retrieves all rows pertaining to the sbider inputTranstion
table using these values the dictionary is created.
Argument(s):
cursor - sqlite3 cursor object instance
Return:
A dictionary mapping input transition id to a species id list.
"""
input_transitions_species_dict = {}
input_transition_species_list = db.db_select(cursor,
"InputTransitionSpecies",
["it_id", "spe_id"])
input_transition_species_list = input_transition_species_list.fetchall()
inserted_it_ids = []
for it_id, spe_id in input_transition_species_list:
if it_id not in inserted_it_ids:
input_transitions_species_dict[it_id] = [spe_id]
inserted_it_ids.append(it_id)
else:
input_transitions_species_dict[it_id].append(spe_id)
return input_transitions_species_dict
def determine_operon_activated_input_transition(cursor, starting_species_list, operon_id):
"""Determining which input transition is activating the operon."""
starting_species_set = set(tuple(starting_species_list))
###print "starting_species_set:", starting_species_set
it_trans_id_list = db.db_select(cursor, "OperonInputTransition", ["it_id"], ["ope_id"], ["="], ["'" + operon_id + "'"], [""])
it_trans_id_list = it_trans_id_list.fetchall()
it_trans_id_list = list_of_lists(it_trans_id_list)
###print "it_trans_id_list:", it_trans_id_list
it_trans_id_list = merge_list_of_lists(it_trans_id_list)
###print "it_trans_id_list:", it_trans_id_list
it_id_dict = get_input_transition_species_dictionary(cursor)
for it_trans_id in it_trans_id_list:
###print "Searching it_trans_list:", it_trans_id
print "it_id_dict[it_trans_id]:", it_id_dict[it_trans_id]
activating_species_set = set(it_id_dict[it_trans_id])
print "activating_species_set:", activating_species_set
if starting_species_set.issuperset(activating_species_set):
return it_trans_id
return None
def create_input_transition_nodes(cursor, starting_species_list, operon_id,
input_transition_id_dict):
"""Create input transition nodes list from the corresponding operon_id.
Argument(s):
cursor - sqlite3 cursor object
starting_species_list - a list of species activating an operon
operon_id - sbider based operon id
input_transition_id_dict - dictionary mapping input transitions to corresponding species
Return:
A tuple of input transition nodes list (with abbreviation) and
input transition id list.
For example:
( [ ("ope_1-1", "pLux-->gfp", "sbol_image_path_1"), ("ope_2-1", "pLambda-->gfp", "sbol_image_path_2"), ... ],
["1-1", "2-1", ...] )
"""
activated_it_ids = determine_operon_activated_input_transition(
cursor, starting_species_list, operon_id, input_transition_id_dict)
it_node_abbrev_list = []
activated_it_id_list = []
for activated_it_id in activated_it_ids:
it_node = db.db_select(cursor, "InputTransition", "*", ["it_id"],
["="], [activated_it_id], [""])
it_node = list(it_node.fetchone())
it_node_abbrev = add_node_id_abbreviation(it_node, "it_", 0)
it_node_abbrev_list.append(it_node_abbrev)
activated_it_id_list.append(activated_it_id)
return it_node_abbrev_list, activated_it_id_list
def determine_operon_activated_input_transition(cursor, starting_species_list,
operon_id,
input_transition_id_dict):
"""Determining which input transition is activating an operon.
Argument(s):
cursor - sqlite3 cursor object
starting_species_list - a list of species activating an operon
operon_id - sbider based operon id
id_id_dict - dictionary mapping input transitions to corresponding species
Return:
A list of transitions that activate the operon (from operon_id).
For example: ["it_1", "it_2", ...]
"""
starting_species_set = set(tuple(starting_species_list))
it_trans_id_list = db.db_select(cursor, "OperonInputTransition", ["it_id"],
["ope_id"], ["="], ["'" + operon_id + "'"],
[""])
it_trans_id_list = it_trans_id_list.fetchall()
it_trans_id_list = list_of_lists(it_trans_id_list)
it_trans_id_list = merge_list_of_lists(it_trans_id_list)
activated_it_id_list = []
for it_trans_id in it_trans_id_list:
activating_species_set = set(input_transition_id_dict[it_trans_id])
if starting_species_set.issuperset(activating_species_set):
activated_it_id_list.append(it_trans_id)
return activated_it_id_list
def get_whole_network(cursor):
"""Whole network data prep for json."""
species_nodes_list = db.db_select(cursor, "Species", ["spe_id", "name", "type"])
species_nodes_list = species_nodes_list.fetchall()
species_nodes_list = list_of_lists(species_nodes_list)
species_nodes_list_abbrev = add_node_list_id_abbreviation(species_nodes_list, "spe_", 0)
input_transition_nodes_list = db.db_select(cursor, "InputTransition", ["it_id", "logic"])
input_transition_nodes_list = input_transition_nodes_list.fetchall()
input_transition_nodes_list = list_of_lists(input_transition_nodes_list)
input_transition_nodes_list_abbrev = add_node_list_id_abbreviation(input_transition_nodes_list, "it_", 0)
operon_nodes_list = db.db_select(cursor, "Operon", ["ope_id", "name"])
operon_nodes_list = operon_nodes_list.fetchall()
operon_nodes_list = list_of_lists(operon_nodes_list)
operon_nodes_list_abbrev = add_node_list_id_abbreviation(operon_nodes_list, "ope_", 0)
output_transition_nodes_list = db.db_select(cursor, "OutputTransition", ["ot_id"])
output_transition_nodes_list = output_transition_nodes_list.fetchall()
output_transition_nodes_list = list_of_lists(output_transition_nodes_list)
output_transition_nodes_list_abbrev = add_node_list_id_abbreviation(output_transition_nodes_list, "ot_", 0)
species_input_transition_edge_list = db.db_select(cursor, "InputTransitionSpecies", ["spe_id", "it_id"])
species_input_transition_edge_list = species_input_transition_edge_list.fetchall()
species_input_transition_edge_list = list_of_lists(species_input_transition_edge_list)
species_input_transition_edge_list_abbrev = add_edge_list_id_abbreviation(species_input_transition_edge_list,
"spe_", "it_")
input_transition_operon_edge_list = db.db_select(cursor, "OperonInputTransition", ["it_id", "ope_id"])
input_transition_operon_edge_list = input_transition_operon_edge_list.fetchall()
input_transition_operon_edge_list = list_of_lists(input_transition_operon_edge_list)
input_transition_operon_edge_list_abbrev = add_edge_list_id_abbreviation(input_transition_operon_edge_list,
"it_", "ope_")
operon_output_transition_edge_list = db.db_select(cursor, "OperonOutputTransition", ["ope_id", "ot_id"])
operon_output_transition_edge_list = operon_output_transition_edge_list.fetchall()
operon_output_transition_edge_list = list_of_lists(operon_output_transition_edge_list)
operon_output_transition_edge_list_abbrev = add_edge_list_id_abbreviation(operon_output_transition_edge_list,
"ope_", "ot_")
output_transition_species_edge_list = db.db_select(cursor, "OutputTransitionSpecies", ["ot_id", "spe_id"])
output_transition_species_edge_list = output_transition_species_edge_list.fetchall()
output_transition_species_edge_list = list_of_lists(output_transition_species_edge_list)
output_transition_species_edge_list_abbrev = add_edge_list_id_abbreviation(output_transition_species_edge_list,
"ot_", "spe_")
all_edges = species_input_transition_edge_list_abbrev + input_transition_operon_edge_list_abbrev + \
operon_output_transition_edge_list_abbrev + output_transition_species_edge_list_abbrev
return (species_nodes_list_abbrev, input_transition_nodes_list_abbrev, operon_nodes_list_abbrev,
output_transition_nodes_list_abbrev, all_edges)
def get_sbml_operons():
'''
Access operon table to retrieve all relevant operon information
@Output: dictionary = {operon id: operon name}
key = operon id: string type
value = operon name: string type
'''
devices = sd.db_select(cursor,'operon',['ope_id','name'])
devices = devices.fetchall()
return dict(devices)
def get_input_transition_species_dictionary(cursor):
input_transitions_species_dict = {}
input_transition_species_list = db.db_select(cursor, "InputTransitionSpecies", ["it_id", "spe_id"])
it_id_list = []
for it_id, spe_id in input_transition_species_list:
if it_id not in it_id_list:
input_transitions_species_dict[it_id] = [spe_id]
it_id_list.append(it_id)
else:
input_transitions_species_dict[it_id].append(spe_id)
return input_transitions_species_dict
def get_sbml_species():
'''
Access chemical species table and retrieve all relevant species information
@Output: dictionary = {species id: species name}
key = species id
value = species name
'''
species = sd.db_select(cursor,'species',['spe_id', 'name'])
species = species.fetchall()
return dict(species)
def get_sbml_input_logic():
'''
Access the input transition logic table and acquire
input transition Boolean logic
@Output: dictionary = {it_id: logic}
key = input transition id
value = associated Boolean logic
'''
in_logic = sd.db_select(cursor, 'InputTransition',['it_id','logic'])
in_logic = in_logic.fetchall()
return dict(in_logic)
def get_sbml_output_operon_edges():
'''
Access the output transition-operon relationship table and acquire
output transition-operon edges
@Output: dictionary = {ot_id: ope_id}
key = output transition id
value = operon id
'''
operon_out_trans = sd.db_select(cursor, 'OperonOutputTransition',['ot_id','ope_id'])
operon_out_trans = operon_out_trans.fetchall()
return dict(operon_out_trans)
def get_sbml_miriam_ids():
'''
Access plasmid table and plasmid-operon relationship table to retrieve
the miriam ids of each operon
@Output: dictionary = {operon id: miriam id}
operon id: string type
miriam id: string type
'''
devices = sd.db_select(cursor,'plasmid',['pla_id', 'PMID'])
devices = devices.fetchall()
plasmid_operon = sd.db_select(cursor,'plasmidoperon',['ope_id','pla_id'])
plasmid_operon = plasmid_operon.fetchall()
plasmid_miriam = dict(devices)
operon_miriam = {}
for operon in plasmid_operon:
operon_id = operon[0]
plasmid_id = operon[1]
if plasmid_id in plasmid_miriam:
operon_miriam[operon_id] = plasmid_miriam[plasmid_id]
return operon_miriam
def get_node_from_id(cursor, node_table_name, node_id, node_id_type):
node_cursor = db.db_select(cursor, node_table_name, "*", [node_id_type], ["="], [node_id], [""])
node = node_cursor.fetchone()
node = list(node)
return node
def create_input_transition_node(cursor, operon_id, starting_species_list):
"""Create input transition nodes from the corresponding operon_id."""
activated_it_id = determine_operon_activated_input_transition(cursor, starting_species_list, operon_id)
###print "activated_it_id:",activated_it_id
it_node = db.db_select(cursor, "InputTransition", "*", ["it_id"], ["="], [activated_it_id], [""])
it_node = list(it_node.fetchone())
it_node_abbrev = add_node_id_abbreviation(it_node, "it_", 0)
###print "it_node_abbrev:", it_node_abbrev
return it_node_abbrev, activated_it_id
def create_input_transition_nodes(cursor, starting_species_list, operon_id, it_id_dict):
"""Create input transition nodes from the corresponding operon_id."""
activated_it_ids = determine_operon_activated_input_transition(cursor, starting_species_list, operon_id, it_id_dict)
it_node_abbrev_list = []
activated_it_id_list = []
for activated_it_id in activated_it_ids:
it_node = db.db_select(cursor, "InputTransition", "*", ["it_id"], ["="], [activated_it_id], [""])
it_node = list(it_node.fetchone())
it_node_abbrev = add_node_id_abbreviation(it_node, "it_", 0)
it_node_abbrev_list.append(it_node_abbrev)
activated_it_id_list.append(activated_it_id)
return it_node_abbrev_list, activated_it_id_list
def get_node_from_id(cursor, node_table_name, node_id, node_id_type):
"""Query the database using the node_id for node.
Argument(s):
cursor - sqlite3 cursor object
node_table_name - table_name where node information exists
node_id - string representation of node_id
node_id_type - the type of node being used from the sbider database.
Return:
A tuple of information representing the node.
"""
node_cursor = db.db_select(cursor, node_table_name, "*", [node_id_type], ["="], [node_id], [""])
node_ = node_cursor.fetchone()
node_ = list(node_)
return node_
def get_node_from_id(cursor, node_table_name, node_id, node_id_type):
"""Query the database using the node_id for node.
Argument(s):
cursor - sqlite3 cursor object
node_table_name - table_name where node information exists
node_id - string representation of node_id
node_id_type - the type of node being used from the sbider database.
Return:
A tuple of information representing the node.
"""
node_cursor = db.db_select(cursor, node_table_name, "*", [node_id_type],
["="], [node_id], [""])
node_ = node_cursor.fetchone()
node_ = list(node_)
return node_
def get_node_from_id(cursor, node_table_name, node_id, node_id_type):
###print "node_table_name:", node_table_name
###print "node_id:", node_id
###print "node_id_type:", node_id_type
node_cursor = db.db_select(cursor, node_table_name,"*", [node_id_type], ["="], [node_id], [""] )
#print "node_cursor:", node_cursor
node = node_cursor.fetchone()
#print "node:", node
node = list(node)
###print "node:", node
return node
def get_sbml_output_species_edges():
'''
Access the output transition-chemical species relationship table and acquire
output species-transition edges
@Output: dictionary = {ot_id: [spe_id]}
key = output transition id
value = list of associated output chemical species
'''
OUT = sd.db_select(cursor,'outputtransitionspecies', ['ot_id','spe_id'])
OUT = OUT.fetchall()
output_trans_species = {}
for trans in OUT:
output_trans_id = trans[0]
species_id = trans[1]
if output_trans_id not in output_trans_species:
output_trans_species[output_trans_id] = []
output_trans_species[output_trans_id].append(species_id)
else:
output_trans_species[output_trans_id].append(species_id)
return output_trans_species
def determine_operon_activated_input_transition(cursor, starting_species_list, operon_id, it_id_dict):
"""Determining which input transition is activating the operon."""
starting_species_set = set(tuple(starting_species_list))
it_trans_id_list = db.db_select(cursor, "OperonInputTransition", ["it_id"], ["ope_id"], ["="],
["'" + operon_id + "'"], [""])
it_trans_id_list = it_trans_id_list.fetchall()
it_trans_id_list = list_of_lists(it_trans_id_list)
it_trans_id_list = merge_list_of_lists(it_trans_id_list)
activated_it_id_list = []
for it_trans_id in it_trans_id_list:
activating_species_set = set(it_id_dict[it_trans_id])
if starting_species_set.issuperset(activating_species_set):
activated_it_id_list.append(it_trans_id)
return activated_it_id_list
def get_input_transition_species_dictionary(cursor):
"""
Retrieves all rows pertaining to the sbider inputTranstion
table using these values the dictionary is created.
Argument(s):
cursor - sqlite3 cursor object instance
Return:
A dictionary mapping input transition id to a species id list.
"""
input_transitions_species_dict = {}
input_transition_species_list = db.db_select(cursor, "InputTransitionSpecies", ["it_id", "spe_id"])
input_transition_species_list = input_transition_species_list.fetchall()
inserted_it_ids = []
for it_id, spe_id in input_transition_species_list:
if it_id not in inserted_it_ids:
input_transitions_species_dict[it_id] = [spe_id]
inserted_it_ids.append(it_id)
else:
input_transitions_species_dict[it_id].append(spe_id)
return input_transitions_species_dict
def get_sbml_input_species_edges():
'''
Access the input transition-chemical species relationship table and acquire
input species-transition edges
@Output: dictionary = {it_id: [(spe_id, repressor_boolean)]}
key = input transition id
value = list of associated input chemical species
tuple = (chemical species, associated repressor boolean). If
chemical species is a repressor then repressor_boolean is 'True'
'''
IN = sd.db_select(cursor,'inputtransitionspecies', ['it_id','spe_id','repression'])
IN = IN.fetchall()
input_trans_species = {}
for trans in IN:
input_trans_id = trans[0]
species_id = trans[1]
repressor_bool = trans[2]
if input_trans_id not in input_trans_species:
input_trans_species[input_trans_id] = []
input_trans_species[input_trans_id].append((species_id,repressor_bool))
else:
input_trans_species[input_trans_id].append((species_id,repressor_bool))
return input_trans_species
def get_whole_network(cursor):
"""Whole network data prep for json."""
species_nodes_list = db.db_select(cursor, "Species",
["spe_id", "name", "type"])
species_nodes_list = species_nodes_list.fetchall()
species_nodes_list = list_of_lists(species_nodes_list)
species_nodes_list_abbrev = add_node_list_id_abbreviation(
species_nodes_list, "spe_", 0)
input_transition_nodes_list = db.db_select(cursor, "InputTransition",
["it_id", "logic"])
input_transition_nodes_list = input_transition_nodes_list.fetchall()
input_transition_nodes_list = list_of_lists(input_transition_nodes_list)
input_transition_nodes_list_abbrev = add_node_list_id_abbreviation(
input_transition_nodes_list, "it_", 0)
operon_nodes_list = db.db_select(cursor, "Operon", ["ope_id", "name"])
operon_nodes_list = operon_nodes_list.fetchall()
operon_nodes_list = list_of_lists(operon_nodes_list)
operon_nodes_list_abbrev = add_node_list_id_abbreviation(
operon_nodes_list, "ope_", 0)
output_transition_nodes_list = db.db_select(cursor, "OutputTransition",
["ot_id"])
output_transition_nodes_list = output_transition_nodes_list.fetchall()
output_transition_nodes_list = list_of_lists(output_transition_nodes_list)
output_transition_nodes_list_abbrev = add_node_list_id_abbreviation(
output_transition_nodes_list, "ot_", 0)
species_input_transition_edge_list = db.db_select(
cursor, "InputTransitionSpecies", ["spe_id", "it_id"])
species_input_transition_edge_list = species_input_transition_edge_list.fetchall(
)
species_input_transition_edge_list = list_of_lists(
species_input_transition_edge_list)
species_input_transition_edge_list_abbrev = add_edge_list_id_abbreviation(
species_input_transition_edge_list, "spe_", "it_")
input_transition_operon_edge_list = db.db_select(cursor,
"OperonInputTransition",
["it_id", "ope_id"])
input_transition_operon_edge_list = input_transition_operon_edge_list.fetchall(
)
input_transition_operon_edge_list = list_of_lists(
input_transition_operon_edge_list)
input_transition_operon_edge_list_abbrev = add_edge_list_id_abbreviation(
input_transition_operon_edge_list, "it_", "ope_")
operon_output_transition_edge_list = db.db_select(
cursor, "OperonOutputTransition", ["ope_id", "ot_id"])
operon_output_transition_edge_list = operon_output_transition_edge_list.fetchall(
)
operon_output_transition_edge_list = list_of_lists(
operon_output_transition_edge_list)
operon_output_transition_edge_list_abbrev = add_edge_list_id_abbreviation(
operon_output_transition_edge_list, "ope_", "ot_")
output_transition_species_edge_list = db.db_select(
cursor, "OutputTransitionSpecies", ["ot_id", "spe_id"])
output_transition_species_edge_list = output_transition_species_edge_list.fetchall(
)
output_transition_species_edge_list = list_of_lists(
output_transition_species_edge_list)
output_transition_species_edge_list_abbrev = add_edge_list_id_abbreviation(
output_transition_species_edge_list, "ot_", "spe_")
all_edges = species_input_transition_edge_list_abbrev + input_transition_operon_edge_list_abbrev + \
operon_output_transition_edge_list_abbrev + output_transition_species_edge_list_abbrev
return (species_nodes_list_abbrev, input_transition_nodes_list_abbrev,
operon_nodes_list_abbrev, output_transition_nodes_list_abbrev,
all_edges)
def get_whole_network(cursor):
"""Whole network data prep for json."""
#*****Gathering all nodes
species_nodes_list = db.db_select(cursor, "Species", ["spe_id", "name", "type"])
species_nodes_list = species_nodes_list.fetchall()
species_nodes_list = list_of_lists(species_nodes_list)
species_nodes_list_abbrev = add_node_list_id_abbreviation(species_nodes_list, "spe_", 0)
#print "species_nodes_list_abbrev:", species_nodes_list_abbrev
input_transition_nodes_list = db.db_select(cursor, "InputTransition", ["it_id", "logic"])
input_transition_nodes_list = input_transition_nodes_list.fetchall()
input_transition_nodes_list = list_of_lists(input_transition_nodes_list)
input_transition_nodes_list_abbrev = add_node_list_id_abbreviation(input_transition_nodes_list, "it_", 0)
#print "input_transition_nodes_list:", input_transition_nodes_list
operon_nodes_list = db.db_select(cursor,"Operon", ["ope_id", "name", "image"])
operon_nodes_list = operon_nodes_list.fetchall()
operon_nodes_list = list_of_lists(operon_nodes_list)
operon_nodes_list_abbrev = add_node_list_id_abbreviation(operon_nodes_list, "ope_", 0)
#print "operon_nodes_list:", operon_nodes_list_abbrev
output_transition_nodes_list = db.db_select(cursor, "OutputTransition", ["ot_id"])
output_transition_nodes_list = output_transition_nodes_list.fetchall()
output_transition_nodes_list = list_of_lists(output_transition_nodes_list)
output_transition_nodes_list_abbrev = add_node_list_id_abbreviation(output_transition_nodes_list, "ot_", 0)
species_nodes_list_abbrev, input_transition_nodes_list_abbrev, operon_nodes_list_abbrev, output_transition_nodes_list_abbrev
#print "output_transition_nodes_list_abbrev:", output_transition_nodes_list_abbrev
#********************************************Gathering all edges#********************************************#
##***********************************************************************************************************#
##***********************************************************************************************************#
species_input_transition_edge_list = db.db_select(cursor,"InputTransitionSpecies", ["spe_id", "it_id"])
species_input_transition_edge_list = species_input_transition_edge_list.fetchall()
species_input_transition_edge_list = list_of_lists(species_input_transition_edge_list)
species_input_transition_edge_list_abbrev = add_edge_list_id_abbreviation(species_input_transition_edge_list,
"spe_", "it_")
#print_list_entries(species_input_transition_edge_list_abbrev)
#print "species_input_transition_edge_list_abbrev:", species_input_transition_edge_list_abbrev
input_transition_operon_edge_list = db.db_select(cursor,"OperonInputTransition", ["it_id", "ope_id"])
input_transition_operon_edge_list = input_transition_operon_edge_list.fetchall()
input_transition_operon_edge_list = list_of_lists(input_transition_operon_edge_list)
input_transition_operon_edge_list_abbrev = add_edge_list_id_abbreviation(input_transition_operon_edge_list,
"it_", "ope_")
#print_list_entries(input_transition_operon_edge_list_abbrev)
#print "input_transition_operon_edge_list_abbrev:", input_transition_operon_edge_list_abbrev
operon_output_transition_edge_list = db.db_select(cursor,"OperonOutputTransition", ["ope_id", "ot_id"])
operon_output_transition_edge_list = operon_output_transition_edge_list.fetchall()
operon_output_transition_edge_list = list_of_lists(operon_output_transition_edge_list)
operon_output_transition_edge_list_abbrev = add_edge_list_id_abbreviation(operon_output_transition_edge_list,
"ope_", "ot_")
#print_list_entries(operon_output_transition_edge_list_abbrev)
#print "operon_output_transition_edge_list_abbrev", operon_output_transition_edge_list_abbrev
output_transition_species_edge_list = db.db_select(cursor,"OutputTransitionSpecies", ["ot_id", "spe_id"])
output_transition_species_edge_list = output_transition_species_edge_list.fetchall()
output_transition_species_edge_list = list_of_lists(output_transition_species_edge_list)
output_transition_species_edge_list_abbrev = add_edge_list_id_abbreviation(output_transition_species_edge_list,
"ot_", "spe_")
#print_list_entries(output_transition_species_edge_list_abbrev)
#print "output_transition_species_edge_list_abbrev:", output_transition_species_edge_list_abbrev
all_edges = species_input_transition_edge_list_abbrev + input_transition_operon_edge_list_abbrev + operon_output_transition_edge_list_abbrev + output_transition_species_edge_list_abbrev
#print "all_edges:",all_edges
return (species_nodes_list_abbrev, input_transition_nodes_list_abbrev, operon_nodes_list_abbrev,
output_transition_nodes_list_abbrev, all_edges)