def determineBestComboFromString(self, best_combo_string, combos,
processed_arguments):
gene_lists = processed_arguments.gene_lists
combine_gene_lists = processed_arguments.rsen_config.combine_gene_lists
analysis_type = processed_arguments.analysisType()
static_features = processed_arguments.static_features
for combo in combos:
feature_set_string = GeneListComboUtility.generateFeatureSetString(
combo, gene_lists, combine_gene_lists, analysis_type,
static_features)
if GeneListComboUtility.combosAreEquivalent(
feature_set_string, best_combo_string):
return combo
raise ValueError(
"Unable to determine feature set from given combo gene list and feature file combo: "
+ best_combo_string +
".\n Please make sure all gene lists and feature files in the combo "
+ "are present in the drug folder.")
def determineSpecificCombos(self, all_combos):
specific_combos = self.inputs.specific_combos
selected_combos = {}
for specific_combo in specific_combos:
for combo in all_combos:
combo_string = self.generateFeatureSetString(combo)
if specific_combo == combo_string and selected_combos.get(combo_string) is None:
selected_combos[combo_string] = combo
else:
equivalent_combos = GeneListComboUtility.combosAreEquivalent(combo_string, specific_combo)
if equivalent_combos and selected_combos.get(combo_string) is None:
selected_combos[combo_string] = combo
selected_combo_names = SafeCastUtil.safeCast(selected_combos.keys(), list)
if len(selected_combo_names) < len(specific_combos):
self.log.warning("Not all specified combos were available in this data folder.\n"
"Specified combos: %s\n Selected combos: %s", specific_combos, selected_combo_names)
else:
self.log.info("Only running analysis on following combos:\n %s", selected_combo_names)
return SafeCastUtil.safeCast(selected_combos.values(), list)