NPInter

class openomics.database.interaction.NPInter(path='http://bigdata.ibp.ac.cn/npinter4/download/', file_resources=None, source_col_name='ncName', target_col_name='tarName', edge_attr=['tarType', 'tissueOrCell', 'tag', 'class', 'level'], filters=None, directed=True, relabel_nodes=None, verbose=False)

Bases: openomics.database.interaction.Interactions

Loads the NPInter database from http://bigdata.ibp.ac.cn/npinter4/ .

Default path: “http://bigdata.ibp.ac.cn/npinter4/download/” . Default file_resources: {

“interaction_NPInterv4.expr.txt”: “file/interaction_NPInterv4.expr.txt.gz”,

}

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.

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