proteobench.modules.denovo.denovo_DDA_HCD module#

De Novo Module DDA-HCD spectra.

class proteobench.modules.denovo.denovo_DDA_HCD.DDAHCDDeNovoModule(token: str, proteobot_repo_name: str = 'Proteobot/Results_denovo_lfq_DDA_HCD', proteobench_repo_name: str = 'Proteobench/Results_denovo_lfq_DDA_HCD')[source]#

Bases: DeNovoModule

De Novo Module.

benchmarking(input_file_loc: any, input_format: str, user_input: dict, all_datapoints: DataFrame, evaluation_type: str = 'mass') → tuple[DataFrame, DataFrame, DataFrame][source]#

Main workflow of the module. Used to benchmark workflow results.

Parameters:

  • input_file_loc (any) – Path to the workflow output file.

  • input_format (str) – Format of the workflow output file.

  • user_input (dict) – User provided parameters for plotting.

  • all_datapoints (pd.DataFrame) – DataFrame containing all datapoints from the proteobench repo.

  • level (str) – The level precision and recall is calculated. Either precision or recall

  • evaluation_type (str) – The evaluation type for precision calculation. Either exact or mass-based

Returns:

Tuple containing the intermediate data structure, all datapoints, and the input DataFrame.

Return type:

tuple[DataFrame, DataFrame, DataFrame]

is_implemented() → bool[source]#

Return whether the module is fully implemented.

Returns:

Always returns True in this implementation.

Return type:

bool

module_id = 'denovo_DDA_HCD'#