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Team:UCSD Software/Documentation
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Revision as of 02:19, 18 October 2014
Topics
Tutorial
API Documentation
Download and view the documentation on github here. A text version of the documentation is shown below:
Help on module Gen_Network:
NAME
Gen_Network - //Title: SBML Network Generator
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/Gen_Network.py
DESCRIPTION
//Description:
Translate entire network model to SBML and store network file
in current working directory
*************************************************
@author: Fernando Contreras
@email: f2contre@gmail.com
@project: SBiDer
@institution: University of California, San Diego
*************************************************
FUNCTIONS
create_whole_network_sbml()
Help on module SBML_Network:
NAME
SBML_Network - //Title: SBML Network Constructor.
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/SBML_Network.py
DESCRIPTION
//Description:
Each class generates a corresponding SBML description of the input information
and appends the information to a list which is then written to file
*************************************************
@author: Fernando Contreras
@email: f2contre@gmail.com
@project: SBiDer
@institution: University of California, San Diego
*************************************************
CLASSES
CloseModel
IntermediateStep
Model
QualitativeSpecies
Transitions
class CloseModel
| Require class, need to append closing SBML statements for network model
|
| Methods defined here:
|
| __init__(self, model_name)
| @Parameter:
| model_name: model object, instantiated using Model class
class IntermediateStep
| Require class, need to append necessary SBML statements for network model
|
| Methods defined here:
|
| __init__(self, model_name)
| @Parameter:
| model_name: model object, instantiated using Model class
class Model
| Creates a model object. When instantiated the class appends all the URLs
| necessary to understand our network model
|
| Methods defined here:
|
| __init__(self, id='SBider_Network')
|
| writeSBML(self, filename)
| @Parameters:
| filename: desired file name for network file
| type: string
|
| @Method:
| Write SBML formatted network model text file. File is then stored in
| the current working directory.
class QualitativeSpecies
| Qualitative species, such as operons and chemical species, constructor
|
| Methods defined here:
|
| __init__(self, id, compartment, name='NONE', maxLevel='1', constant='false', miriam_id='NONE')
| @Parameters:
| id: node id
| compartment: node compartment, for example, operons belong in the plasmid compartment
| name: node name, default=NONE because operons don't have a name
| maxLevel: node threshold, default = 1 because a logic model was implemented
| constant: denotes node passivity, if constant = True then the node does not interact with
| network. Thus, the node does not transfer information.
| miriam_id: Minimal Information Required in the Annotation of Models id. This allows for
| a standarized citation of literature references
|
| @Method:
| Translate all the inputed information to SBML and append to list
|
| appendToQualSpecies(self, model_name)
class Transitions
| Input and output transition constructor; transitions denote the operon's input
| and output reaction in our network.
|
| Methods defined here:
|
| input_transition(self, model_name, trans_id, input_id_boolean_tuple, operon_id, trans_logic)
| @Parameters:
| node_name: name of node object, instantiated using the Node class
| trans_id: transition id
| input_id_boolean_tuple: tuple of the form (input chemical species, repressor boolean)
| input chemical species: chemical species involved in reaction
| repressor boolean: denotes whether a chemical species is a repressor (True or False)
| Can input a list if multiple operators are involved, such is the case for an AND gate
| operon_id: operon id
| trans_logic: transition logic denotes the Boolean logic of a reaction ('AND', 'OR', 'NOT')
|
| @Method:
| Translate all the inputed information to SBML and append to list
|
| output_transition(self, model_name, trans_id, output_id, operon_id)
| @Parameters:
| node_name: name of node object, instantiated using the Node class
| trans_id: transition id
| output_id: single variable input which denotes the id of an operon's output
| operon_id: operon id
|
| @Method:
| Translate all the inputed information to SBML and append to list
Help on module SBML_Nodes:
NAME
SBML_Nodes - //Title: SBML Node Constructor.
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/SBML_Nodes.py
DESCRIPTION
//Description:
Each class generates a corresponding SBML description of the input information.
*************************************************
@author: Fernando Contreras
@email: f2contre@gmail.com
@project: SBiDer
@institution: University of California, San Diego
*************************************************
CLASSES
Nodes
QualitativeSpecies
Transitions
class Nodes
| Place, passive component of Petri Net model, and transition, active component
| of Petri Net model, file constructor.When instantiated, a qualitative species
| list and a transitions list are created. Data is then stored according to
| SBML standards.
|
| Methods defined here:
|
| __init__(self)
| Instantiate qualitative species and transitions list objects
|
| writeQualSpecies(self, filename)
| @Parameters: filename
| type: string
| description: desired file name for a particular qualitative species
| SBML text file(i.e. operon or chemical species)
| @Method:
| Write SBML text file for a qualitative species stored in the qualitative
| species list object. File is then stored in the current working directory.
|
| writeTransition(self, filename)
| @Parameters: filename
| type: string
| description: desired file name for a particular transition SBML text
| file(i.e. input transition or output transition)
| @Method:
| Write SBML text file for a transition stored in the transition list
| object. File is then stored in the current working directory.
class QualitativeSpecies
| Qualitative species, such as operons and chemical species, constructor
|
| Methods defined here:
|
| __init__(self, id, compartment, name='NONE', maxLevel='1', constant='false', miriam_id='NONE')
| @Parameters:
| id: node id
| compartment: node compartment, for example, operons belong in the plasmid compartment
| name: node name, default=NONE because operons don't have a name
| maxLevel: node threshold, default = 1 because a logic model was implemented
| constant: denotes node passivity, if constant = True then the node does not interact with
| network. Thus, the node does not transfer information.
| miriam_id: Minimal Information Required in the Annotation of Models id. This allows for
| a standarized citation of literature references
|
| @Method:
| Translate all the inputed information to SBML and append to list
|
| appendToQualSpecies(self, node_name)
class Transitions
| Input and output transition constructor; transitions denote the operon's input
| and output reaction in our network.
|
| Methods defined here:
|
| input_transition(self, node_name, trans_id, input_id_boolean_tuple, operon_id, trans_logic)
| @Parameters:
| node_name: name of node object, instantiated using the Node class
| trans_id: transition id
| input_id_boolean_tuple: tuple of the form (input chemical species, repressor boolean)
| input chemical species: chemical species involved in reaction
| repressor boolean: denotes whether a chemical species is a repressor (True or False)
| Can input a list if multiple operators are involved, such is the case for an AND gate
| operon_id: operon id
| trans_logic: transition logic denotes the Boolean logic of a reaction ('AND', 'OR', 'NOT')
|
| @Method:
| Translate all the inputed information to SBML and append to list
|
| output_transition(self, node_name, trans_id, output_id, operon_id)
| @Parameters:
| node_name: name of node object, instantiated using the Node class
| trans_id: transition id
| output_id: single variable input which denotes the id of an operon's output
| operon_id: operon id
|
| @Method:
| Translate all the inputed information to SBML and append to list
Help on module helper:
NAME
helper - Useful helper functions.
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/helper.py
DESCRIPTION
******************************************************************************
@author: Huwate(Kwat) Yeerna, University of California, San Diego
Joaquin Reina, University of California, San Diego
******************************************************************************
FUNCTIONS
activated(inp_dic, ope, spe)
Check if there is an activation signal for a operon.
:param inp_dic: dictionary of operon and their activation requirement.
:param ope: operon whose activation signal is checked.
:param spe: species that may induce activation signal for the operon.
:return: True only if species match any of the activation requirement of an operon, False otherwise.
contain_all_elements(list_of_lists, lst)
Check if a list that matches the specified list.
:param list_of_lists: list whose inner lists are checked.
:param lst: list matched
:return: True only if the list_of_lists contain a list that matches lst.
contain_an_element(lst1, lst2)
Check if at least on of the elements is a list is in another list.
:param lst1: list that may contain at least one element from anther list.
:param lst2: list whose elements are searched for in another list.
:return: True only if at least an element from lst2 in found in lst1.
format_values(value_list)
Create a list by adding elements of a list in a standard expression.
:param value_list: list whose elements with non-standard expression are reformatted and added to the new list.
:return: a new list with elements in standard expression.
get_matching_list_and_index(list_of_lists, lst)
Get a matching list within a list of lists that matches a specified list.
:param list_of_lists: list whose inner lists are checked to see if any of them match the specified list.
:param lst: list checked.
:return: list within list_of_lists that matches the specified list.
list_is_type(lst, typ)
Check if all elements of a list are the specified type.
:param lst: list whose elements are checked.
:param typ: type specified.
:return: True only if all elements of the list is the specified type, False otherwise.
match_any_list(list_of_lists, lst)
Check if a list matches any of the lists within a list of lists.
:param list_of_lists: list of lists that contain potential matching lists.
:param lst: list matched.
:return: True only is at least a list within the list of lists matches the specified list.
promoter_activation(inp_dic, rep_dic, ope, spe, memory_spe, indirect_flag)
Check if a promoter is activated.
:param inp_dic: dictionary of operon and their activation requirement.
:param rep_dic: dictionary of operon and their repression requirement.
:param ope: operon whose activation is checked.
:param spe: species that can activate or repress an operon.
:param memory_spe: species that can activate or repress an operon.
:param indirect_flag: Boolean flag for checking indirect activation of an operon
:return: True if the operon is activated.
remove_duplicated_lists_within_a_list_of_lists(list_of_lists)
Create a list that contains unique lists within another list.
:param list_of_lists: list that contains duplicated lists.
:return: list that contains unique lists from the list.
remove_duplicates_within_list(lst)
Create a list with only unique elements form another list.
:param lst: list whose unique elements will be stored in a new list.
:return: a list that contains non-duplicated elements from the parameter list.
remove_parentheses(sequence)
Remove the outermost parentheses of a string, and return the element right after the closing parentheses.
:param sequence:
:return:
repressed(rep_dic, ope, spe)
Check if there is an repression signal for a operon.
:param rep_dic: dictionary of operon and their repression requirement.
:param ope: operon whose repression signal is checked.
:param spe: species that may induce repression signal for the operon.
:return: True only if species match any of the repression requirement of an operon, False otherwise.
reverse_index(sequence, element)
Find the last occurring index of an element in a sequence.
:param sequence: list checked.
:param element: element searched.
:return: index of the last occurring index of an element.
split_by(sequence, element)
Split a sequence by the first occurring index of a specified element, and return the the resulting two-halves of
the sequence in a dictionary.
:param sequence: sequence that is split.
:param element: element whose first occurring index splits the sequence.
:return: dictionary that contains the split two halves of the sequence.
uniquely_merge_list_of_lists(list_of_lists)
Create a list that contain unique elements from lists within itself.
:param list_of_lists: list that contains lists
:return: list that contains unique elements from lists within the list.
uniquely_merge_multi_dimensional_list_of_lists(multi_dimensional_list_of_lists)
Create a list that contain unique elements from lists within itself.
:param multi_dimensional_list_of_lists: list that contains lists
:return: list that contains unique elements from lists within the list.
Help on module node:
NAME
node - Subtitle
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/node.py
DESCRIPTION
Descriptive paragraph
******************************************************************************
@author: Huwate(Kwat) Yeerna, University of California, San Diego
******************************************************************************
CLASSES
__builtin__.object
Node
class Node(__builtin__.object)
| Methods defined here:
|
| __init__(self, value)
|
| __repr__(self, level=0)
|
| append_child(self, obj)
|
| get_all_leaf(self)
|
| get_path_from_all_leaf(self)
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
Help on module sbider_database:
NAME
sbider_database - Subtitle
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/sbider_database.py
DESCRIPTION
Descriptive paragraph
******************************************************************************
@author: Huwate(Kwat) Yeerna, University of California, San Diego
Joaquin Reina, University of California, San Diego
******************************************************************************
FUNCTIONS
db_close(connection, cursor)
Close a database.
db_create_table(cursor)
Make tables for sbider.db
db_custom(cursor, sql_command)
Do whatever.
db_delete(cursor, table_name)
Delete table contents.
db_drop_all_table(cursor)
Drop all tables.
db_drop_table(cursor, table_name)
Drop a table.
db_get_operon_id_from_name(cursor, operon_name)
db_get_operon_name_from_id(cursor, operon_id)
db_get_plasmid_id_from_name(cursor, plasmid_name)
db_get_plasmid_name_from_id(cursor, plasmid_id)
db_get_species_id_from_name(cursor, species_name)
db_get_species_name_from_id(cursor, species_id)
db_insert(cursor, table_name, table_header_list, insert_data_list)
Insert into a table.
Args:
table_name, that table that you wish to insert into
cols, the columns that you want to insert into
new_row, the values that correspond to the columns
Examples:
ex 1. Inserting into plasmid table and filling in all the columns.
db_open(database_file)
Connect to a database or create a database if it does not already
exist.
db_print_all_table(cursor)
Print all tables.
db_print_table(cursor, table_name)
Print a table.
db_select(cursor, table_name, table_header_list, where_columns=None, where_options=None, where_values=None, where_bools=None, group=None, having_columns=None, having_bools=None, having_values=None)
Select from a table.
Argument(s):
table_name: table you wish to pull data from
col_names: list of numbers indexing the table columns
w_col: column names for where clause
w_opt: operator for where clause
w_var: variable for where clause
w_bool: boolean for where clause
group: group name for GROUP BY clause
h_col: group specifier
Return:
db_update(cursor, table_name, table_header_list, update_data_list, where_column='', where_option='', where_value='')
Update.
get_all_input_transition_species(cursor, input_transition_id)
Obtain all species an input transition takes.
get_all_output_transition_species(cursor, input_transition_id)
Obtain all species an output transition produces.
make_input_ope_id_spe_id_dic(cursor)
Make operon input species dictionary.
make_ope_id_rep_spe_id_dic(cursor)
Make operon input not dictionary.
make_ope_id_spe_id_dics(cursor)
make_output_ope_id_spe_id_dic(cursor)
Make operon output species dictionary.
make_pla_name_spe_name_dics(cursor)
Make operon input and output species dictionary.
make_plasmid_species_name_dictionary(cursor, operon_id_plasmid_name_dictionary, operon_species_dictionary)
make_sql_delete_command(table_name)
make_sql_drop_command(table_name)
make_sql_insert_command(table_name, table_header_list, insert_data_list)
Make SQL insert command.
make_sql_select_command(table_name, table_header_list, where_columns=None, where_options=None, where_values=None, where_bools=None, group=None, having_columns=None, having_bools=None, having_values=None)
Make SQL select command.
@param table_header_list - list of columns to be selected
@param where_columns - column names for where clause
@param where_options - operator for where clause
@param where_values - variable for where clause
@param where_bools - boolean for where clause
@param group - group name for GROUP BY clause
@param having_columns
make_sql_update_command(table_name, table_header_list, update_data_list, where_column='', where_option='', where_value='')
Makes SQL update command
@param table_name - Updating table
@param table_header_list - Selected columns
@param where_columns - Where column names
@param where_options - List of operators
@param where_values - variable for where clause
@param where_bools - boolean for where clause
Help on module sbider_grapher:
NAME
sbider_grapher - Subtitle
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/sbider_grapher.py
DESCRIPTION
Descriptive paragraph
******************************************************************************
@author: Joaquin Reyna, University of California, San Diego
Huwate(Kwat) Yeerna, University of California, San Diego
******************************************************************************
FUNCTIONS
add_edge_id_abbreviation(edge, abbrev1, abbrev2, index1=0, index2=0)
add_edge_list_id_abbreviation(edge_list, abbrev1, abbrev2, index1=0, index2=0)
add_node_id_abbreviation(node_, abbrev, index)
Adds an id abbreviation to a node.
Argument(s):
node - list representing node information.
abbrev - string abbreviation.
index - integer indicating which value to abbreviate.
Return:
A node with the abbreviation added to the given index.
For example: [ "abbreviation_node_id", "node_field_2", "node_field_3", ...]
add_node_list_id_abbreviation(node_list, abbrev, id_index)
Adds an id abbreviation to a list of nodes.
Argument(s):
node_list - list containing nodes.
abbrev - string abbreviation.
index - integer indicating which value to abbreviate.
Return:
A node_list the abbreviation added to the given index
of every node.
For example: [ [ "abbreviation_node_id_1", "node_field_2", "node_field_3", ...],
[ "abbreviation_node_id_2", "node_field_2", "node_field_3", ...], ...]
add_node_values_to_nxgraph(nxgraph, node_list)
Extracts the node id and enters it into nxGraph.
create_input_species_nodes(cursor, it_id)
Create species nodes from the corresponding it_id.
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", ...] )
create_json_network_file(json_file_path, species_nodes_list, input_transitions_nodes_list, operon_nodes_list, output_transitions_nodes_list, source_id_target_id_list)
Writes the whole network json.
:param json_file_path:
:param species_nodes_list:
:param input_transitions_nodes_list:
:param operon_nodes_list:
:param output_transitions_nodes_list:
:param source_id_target_id_list:
create_json_network_string(species_nodes_list, input_transitions_nodes_list, operon_nodes_list, output_transitions_nodes_list, source_id_target_id_list, path_json_highlighter)
create_json_whole_network_file(file_name, cursor)
Generates the whole network json.
create_operon_node(cursor, operon_id)
Create an operon node from the corresponding operon_id.
Argument(s):
cursor - sqlite 3 cursor object.
operon_id - sbider based operon id
Return:
A tuple with operon node information as a tuple
(id abbrevation included) and the corresponding
operon id.
For example: ( ("ope_1-1", "pLux-->gfp", "sbol_image_path_1"), "1-1" )
create_output_species_nodes(cursor, ot_id)
Create species nodes from the corresponding ot_id.
create_output_transition_node(cursor, operon_id)
Create output transition nodes from the corresponding operon_id.
Argument(s):
cursor - sqlite3 cursor object
operon_id - sbider based operon id
Return:
A list of tuples with operon node information.
create_subnetwork_json_string(cursor, list_of_operon_paths)
Generates the subnetwork json.
create_subnetwork_path(cursor, starting_species_list, operon_path, it_trans_dict)
Creating a subnetwork path.
:rtype : object
:param cursor:
:param starting_species_list:
:param operon_path:
:param it_trans_dict:
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", ...]
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.
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.
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.
get_path_json_array(cursor, starting_species_list, operon_paths_list)
Generate json array for node highlighting.
get_subnetwork(cursor, list_of_operon_paths)
get_whole_network(cursor)
Whole network data prep for json.
list_of_lists(list_of_tups)
Creates a list of lists from a list of tuples.
Return:
A list with list values.
list_of_tuples(list_of_lsts)
Creates a list of tuples from a list of lists.
Return:
A list with tuple values.
merge_list_of_lists(list_of_lsts)
ALREADY EXISTS IN THE HELPER!!
nx_node_coordinates_dictionary(node_id_list, edge_list)
Creates a dictionary of node coordinates using spring layout from networkx.
Argument(s):
node_id_list - ids of nodes for positioning
edge_list - all edges between nodes stored in a tuple as follows,
(source_node_id, target_node_id)
Return:
A dictionary mapping
resize_network(total_subnetwork_nodes, total_whole_nodes=540)
Resize the network.
unique_node_list(nodes_list)
Removal of duplicate nodes from the node_list.
Argument(s):
node_list - list of node information stored as list (list of lists).
Return:
A list of unique nodes.
For example:
[ ["node_id_1", "node_field_2", "node_field_3"], ["node_id_2", "node_field_2", "node_field_3", ...], ...]
Help on module sbider_network_builder:
NAME
sbider_network_builder - Subtitle
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/sbider_network_builder.py
DESCRIPTION
Descriptive paragraph
******************************************************************************
@author: Huwate(Kwat) Yeerna, University of California, San Diego
Joaquin Reyna, University of California, San Diego
******************************************************************************
FUNCTIONS
build_sbider_network(directory_path, user_query, indirect=False)
Help on module sbider_parser:
NAME
sbider_parser - Subtitle
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/sbider_parser.py
DESCRIPTION
Descriptive paragraph
******************************************************************************
@author: Huwate(Kwat) Yeerna, University of California, San Diego
******************************************************************************
FUNCTIONS
grammar_0(cursor, tokens)
Grammar for 'grammar_0:= grammar_1 > grammar_1'.
:param cursor:
:param tokens:
:return:
grammar_1(cursor, tokens)
Grammar for 'grammar_1:= grammar_2 or grammar_1 |
grammar_2 and grammar_1 |
grammar_2'.
:param cursor:
:param tokens:
:return:
grammar_2(cursor, tokens)
Grammar for 'grammar_2:= (grammar_1) or grammar_1 |
(grammar_1) and grammar_1 |
(grammar_1) |
interactor'.
:param cursor:
:param tokens:
:return:
grammar_and(tokens1, tokens2)
Grammar for 'and'.
:param tokens1:
:param tokens2:
:return:
grammar_or(tokens1, tokens2)
Grammar for 'or'.
:param tokens1:
:param tokens2:
:return:
grammar_output(tokens1, tokens2)
Grammar for '='.
:param tokens1:
:param tokens2:
:return:
interactor(cursor, token)
Grammar for 'interactor'.
:param cursor:
:param token:
:return:
parse_logic(cursor, logic_input)
Parse a logic input into atomized and equivalent logic.
:param cursor:
:param logic_input:
:return:
Help on module sbider_searcher:
NAME
sbider_searcher - Subtitle
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/sbider_searcher.py
DESCRIPTION
Descriptive paragraph
******************************************************************************
@author: Huwate(Kwat) Yeerna, University of California, San Diego
Joaquin Reina, University of California, San Diego
******************************************************************************
FUNCTIONS
build_direct_sbider_path(input_dictionary, repressor_dictionary, output_dictionary, input_species_list, output_species_list, path_queue, final_operon_path_list, memory_operon, memory_species, activated_paths, indirect_flag)
build_indirect_sbider_path(input_dictionary, repressor_dictionary, output_dictionary, input_species_list, output_species_list, path_queue, final_operon_path_list, memory_operon, memory_species, activated_paths)
build_sbider_path_memory_tree(input_dictionary, activated_paths, start_operon)
get_sbider_path(inp_dic, rep_dic, outp_dic, inp_spe, outp_spe, indirect_flag=False)
search_sbider_path_memory(input_dictionary, activated_paths, from_operon)
Help on module sbider_upload_database:
NAME
sbider_upload_database
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/sbider_upload_database.py
FUNCTIONS
check_species_name_in_database(cursor, species_name)
Safely return species id or None.
db_test()
determine_and_insert(connection, cursor, component_keyword, component_data=[], parent_component_id='')
Determine insertion method and insert into into the database.
determine_parent_keyword(component_keyword)
Determine which is your parent keyword.
get_data_keyword(data_string)
Get the keyword belonging to data_string.
get_last_row_id(cursor, table_name)
Get the last inserted rowid.
insert_new_device(connection, cursor, device)
Inserts a new device into the database.
Argument(s):
connection - sqlite3 connection object
cursor - sqlite3 cursor object
device_string - whole device as a string
insert_new_input_transition(cursor, operon_id, logic)
Insert new input transition.
insert_new_input_transition_species(cursor, it_id, species_name, species_type, species_repression)
Insert new input transition species.
insert_new_operon(cursor, plasmid_id, operon_name, direction)
Insert new operon.
insert_new_output_transition(cursor, operon_id)
Insert new output transition.
insert_new_output_transition_species(cursor, ot_id, species_name, species_type)
Insert new output transition species.
insert_new_plasmid(cursor, plasmid_name, miriam_id)
Insert new plasmid.
main()
make_input_transition_sbml_file(input_species_list, transition_id, operon_id, trans_logic)
make_new_id(id_string)
Convert old string id to old string id + 1.
make_output_transition_sbml_file(output_species_list, transition_id, operon_id)
make the sbml.
make_sbol_file(output_species_list, promoter_list, prev_operon_direction, operon_id)
Insert and make the sbol file.
make_sbol_string_db_update(input_list, direction)
Make an sbol string using uploading information.
reset_db(original_db='sbider.db', test_db_file='sbider_test_2.db')
select_last_inserted_table_id(cursor, table_name, table_id_type)
Select the last inserted row.
select_last_inserted_table_row(cursor, table_name)
Select the last inserted row.
write_sbol_file(operon_id, sbol_string)
Write out sbol string to file.
write_to_file(string_to_write, file_name)
Write a file.
Help on module sbml_database:
NAME
sbml_database - //Title: SBML Database Access
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/sbml_database.py
DESCRIPTION
//Description:
Access SBiDer database and retrieve all necessary SBML information
*************************************************
@author: Fernando Contreras
@email: f2contre@gmail.com
@project: SBiDer
@institution: University of California, San Diego
*************************************************
FUNCTIONS
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
get_sbml_input_operon_edges()
Access the input transition-operon relationship table and acquire
input transition-operon edges
@Output: dictionary = {it_id: ope_id}
key = input transition id
value = operon id
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'
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
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
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
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
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
DATA
con =
cursor =
cwd = '/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web'
database_path = '/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/w...
Help on module sbml_update:
NAME
sbml_update - //Title: SBML Node Generator
FILE
/Users/jenhantao/Documents/UCSD_IGEM/CircuitNetwork/web/sbml_update.py
DESCRIPTION
//Description:
Translate individual node information to SBML and store node file
in current working directory
*************************************************
@author: Fernando Contreras
@email: f2contre@gmail.com
@project: SBiDer
@institution: University of California, San Diego
*************************************************
FUNCTIONS
sbml_input_trans(trans_id, input_species_id_and_boolean_tuple, operon_id, trans_logic, filename)
#construct input/output transition component of network SBML file
sbml_operon(operon_id, operon_name, miriam_id, filename)
#construct operon/chemical species component of network SBML file
sbml_output_trans(trans_id, output_species_id, operon_id, filename)
sbml_species(species_id, species_name, filename)
