API (clue_api_client)

To use the CLUE API client, put a copy of the file example_cmapPy_config_file.cfg in your home directory and name the copy .cmapPy.cfg. Replace the clue_api_user_key entries in that file with your CLUE API user key that you obtained from the CLUE website.

class cmapPy.clue_api_client.clue_api_client.ClueApiClient(base_url=None, user_key=None)

Basic class for running queries against CLUE api

run_count_query(resource_name, where_clause)

run a query (get) against CLUE api

Args:

resource_name: str - name of the resource / collection to query - e.g. genes, perts, cells etc. where_clause: dictionary - contains where clause to pass to API to; uses loopback specification

Returns: dictionary containing the results of the query

run_filter_query(resource_name, filter_clause)

run a query (get) against the CLUE api, using the API and user key fields of self and the fitler_clause provided

Args:

resource_name: str - name of the resource / collection to query - e.g. genes, perts, cells etc. filter_clause: dictionary - contains filter to pass to API to; uses loopback specification

Returns: list of dictionaries containing the results of the query

cmapPy.clue_api_client.gene_queries.are_genes_in_api(my_clue_api_client, gene_symbols)

determine if genes are present in the API

Args:

my_clue_api_client: gene_symbols: collection of gene symbols to query the API with

Returns: set of the found gene symbols