General Functions

This page provides a detailed documentation of ACCORDION general functions, defined under (runAccordion)

loading baseline model

runAccordion.get_model(model_file)

This function reads the baseline model of BioRECIPES format and returns two useful dictionaries

Parameters:

model_file (str) – The path of the baseline model file

Returns:

• model_dict (dict) – Dictionary that holds critical information of each baseline model element

• regulators (dict) – Contains baseline model elements and corresponding regulator elements

matching element names

runAccordion.getVariableName(model_dict, curr_map, ext_element_info)

A utility function for parseExtension(), which matches the element name from the extracted event to an element in the baseline model

Parameters:

• model_dict (dict) – Dictionary that holds critical information of each baseline model element

• curr_map (dict) – Temporary dictionary that contains already matched pairs

• ext_element_info (list) – List of information for certain element in the extracted event, starting with element name

Returns:

match – The most likely matched element name in model_dict, to the element represented by ext_element_info; Otherwise, return the extended element name suffix by “_ext”

Return type:

str

parsing extension

runAccordion.parseExtension(model_dict, ext_file)

This function parses the interactions within the reading output file (extracted events) into a set object, each component in the set has compatible format for BioRECIPES.

Parameters:

• model_dict (dict) – Dictionary that holds critical information of each baseline model element

• ext_file (str) – The path of the reading output file (extracted events)

Returns:

ext_edges – Each interaction within the reading output file will have the form: (regulator element, regulated element, type of interaction (+/-))

Return type:

set

merging clusters

runAccordion.merge_clusters(regulators, path, ReturnTh)

This function records indices of clusters to be merged based on the existence of return paths. It generates the grouped_ext_Merged pickle file that contains the merged clusters.

Parameters:

• regulators (dict) – Contains baseline model elements and corresponding regulator elements

• path (str) – The path of the directory that contains the grouped_ext file

• ReturnTh (int) – A user-defined integer threshold for the number of return paths, beyond which clusters will be merged

generating directed graph

runAccordion.makeDiGraphBase(regulators)

A utility function for merge_clusters(), this function converts the baseline model into a directed graph.

Parameters:

regulators (dict) – Contains baseline model elements and corresponding regulator elements

Returns:

G – Directed graph of the baseline model

Return type:

DiGraph()

indexing model rows

runAccordion.getRow(mdl)

A utility function for extend_model(), this function returns a dict indicating the row of each element of the parsed model.

Parameters:

mdl (str) – The path that will be used to store new extended model spreadsheet

Returns:

• res (dict)

• A dict indicating the row number of each element

extending model by cluster

runAccordion.extend_model(base_mdl, clusters, ext_mdl)

This function creates a new xlsx for each candidate model (i.e. baseline model + cluster)

Parameters:

• base_mdl (str) – The path that contains the baseline model spreadsheet to be extended

• clusters (list) – It holds the edges inside each grouped extension

• ext_mdl (str) – The path that will be used to store new extended model spreadsheet