TargetScan

class openomics.database.interaction.TargetScan(path='http://www.targetscan.org/vert_72/vert_72_data_download/', file_resources=None, source_col_name='MiRBase ID', target_col_name='Gene Symbol', edge_attr=['tissue', 'positive_negative'], directed=True, relabel_nodes=None, species_id=None, strip_mirna_name=False, **kwargs)

Bases: openomics.database.interaction.Interactions, openomics.database.base.Database

Loads the TargetScan database from “http://www.targetscan.org/” .

Default path: “http://www.targetscan.org/vert_72/vert_72_data_download/” . Default file_resources: {

“miR_Family_Info.txt”: “miR_Family_Info.txt.zip”, “Predicted_Targets_Info.default_predictions.txt”: “Predicted_Targets_Info.default_predictions.txt.zip”, “”: “”,

}

Methods Summary

load_network(file_resources, ...[, blocksize])	Handles data processing from file_resources to a Pandas DataFrame which contain edgelist data, then constructs and return a NetworkX Graph.
process_interactions_table(file_resources, ...)	This functions joins the interactions data table between miR Family and targets, and :param file_resources: :param family_to_miR_df: :param species_id:
process_miR_family_info_table(file_resources)

Methods Documentation

load_network(file_resources, source_col_name, target_col_name, edge_attr, directed, filters, blocksize=None)

Handles data processing from file_resources to a Pandas DataFrame which contain edgelist data, then constructs and return a NetworkX Graph. :param file_resources: a dict of file name and file path/object :param source_col_name: column name of the dataframe for source in the edge :type source_col_name: str :param target_col_name: column name of the dataframe for target in the edge :type target_col_name: str :param edge_attr: list of str for column data to include in each edge :type edge_attr: list :param directed: True to return a DiGraph(), else Graph() :type directed: bool :param filters: A dict of {column name: column values} to filter the dataframe :param blocksize ():

Returns

a NetworkX Graph or DiGraph

Return type

network

process_interactions_table(file_resources, family_to_miR_df, species_id)

This functions joins the interactions data table between miR Family and targets, and :param file_resources: :param family_to_miR_df: :param species_id:

Returns:

process_miR_family_info_table(file_resources, species=None)