diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py index 599be5a98fddc4bb60b1488714d4187b31798097..c7554d2cc03dd610e69719d804795b085a26ad06 100644 --- a/cami_src/cami_suite.py +++ b/cami_src/cami_suite.py @@ -349,38 +349,13 @@ class cami(): for tool in result_sets: result_sets[tool] -= set(self.seed_lst) - params_1 = {'consens_threshold': [consens_threshold], - 'function': {'cami_v1': cami_v1.run_cami}} - - params_0 = {'function': {'union':cami_v1.make_union, - 'intersection':cami_v1.make_intersection, - 'first_neighbours': cami_v1.make_first_neighbor_result_set} - } - - params_tr = {'hub_penalty': [0.5], - 'damping_factor': [0.5], + params_tr = {'hub_penalty': [0.25], + 'damping_factor': [0.7], 'confidence_level': [0.5], 'ranking': ['trustrank'], - 'function': {'cami_v2': cami_v2.run_cami, - 'cami_v3':cami_v3.run_cami}} - - params_b_m = {'hub_penalty': [0.5], - 'confidence_level': [0.5], - 'ranking': ['betweenness', 'harmonic'], - 'function': {'cami_v2': cami_v2.run_cami, - 'cami_v3':cami_v3.run_cami}} - - # params_b_m = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0], - # 'confidence_level': [0.2, 0.35, 0.5, 0.75], - # 'ranking': ['betweenness', 'harmonic'], - # 'function': {'cami_v2': cami_v2.run_cami, - # 'cami_v3':cami_v3.run_cami}} + 'function': {'cami_v3':cami_v3.run_cami}} - c = generate_param_combinations(params_0) - cami_setting_list = generate_param_combinations(params_0)+\ - generate_param_combinations(params_1)+\ - generate_param_combinations(params_tr)+\ - generate_param_combinations(params_b_m) + cami_setting_list = generate_param_combinations(params_tr) camis = {} for setting in cami_setting_list: @@ -390,48 +365,6 @@ class cami(): func_name = setting[0] camis[func_name] = setting[2] - # camis = { - # 'union': {'function': cami_v1.make_union, 'params': {}}, - # 'intersection': {'function': cami_v1.make_intersection, 'params': {}}, - # 'first_neighbors': {'function': cami_v1.make_first_neighbor_result_set, 'params': {}}, - # 'cami_v1': {'function': cami_v1.run_cami, 'params': {'consens_threshold': consens_threshold}}, - # 'cami_v2_param1_tr': {'function': cami_v2.run_cami, 'params': { - # 'hub_penalty': 0.3, 'damping_factor': 0.7, 'confidence_level': 0.5 - # }}, - # 'cami_v2_param1_b': {'function': cami_v2.run_cami, 'params': { - # 'hub_penalty': 0.3, 'damping_factor': 0.7, 'ranking': 'betweenness', 'confidence_level': 0.5 - # }}, - # 'cami_v2_param1_hc': {'function': cami_v2.run_cami, 'params': { - # 'hub_penalty': 0.3, 'damping_factor': 0.7, 'ranking': 'harmonic', 'confidence_level': 0.5 - # }}, - # 'cami_v2_param2_tr': {'function': cami_v2.run_cami, 'params': { - # 'hub_penalty': 0, 'damping_factor': 0.7, 'confidence_level': 0.5 - # }}, - # 'cami_v2_param2_b': {'function': cami_v2.run_cami, 'params': { - # 'hub_penalty': 0, 'damping_factor': 0.7, 'ranking': 'betweenness', 'confidence_level': 0.5 - # }}, - # 'cami_v2_param2_hc': {'function': cami_v2.run_cami, 'params': { - # 'hub_penalty': 0, 'damping_factor': 0.7, 'ranking': 'harmonic', 'confidence_level': 0.5 - # }}, - # 'cami_v3_param1_tr': {'function': cami_v3.run_cami, 'params': { - # 'hub_penalty': 0.3, 'damping_factor': 0.7, 'confidence_level': 0.5 - # }}, - # 'cami_v3_param1_b': {'function': cami_v3.run_cami, 'params': { - # 'hub_penalty': 0.3, 'damping_factor': 0.7, 'ranking': 'betweenness', 'confidence_level': 0.5 - # }}, - # 'cami_v3_param1_hc': {'function': cami_v3.run_cami, 'params': { - # 'hub_penalty': 0.3, 'damping_factor': 0.7, 'ranking': 'harmonic', 'confidence_level': 0.5 - # }}, - # 'cami_v3_param2_tr': {'function': cami_v3.run_cami, 'params': { - # 'hub_penalty': 0, 'damping_factor': 0.7, 'confidence_level': 0.5 - # }}, - # 'cami_v3_param2_b': {'function': cami_v3.run_cami, 'params': { - # 'hub_penalty': 0, 'damping_factor': 0.7, 'ranking': 'betweenness', 'confidence_level': 0.5 - # }}, - # 'cami_v3_param2_hc': {'function': cami_v3.run_cami, 'params': { - # 'hub_penalty': 0, 'damping_factor': 0.7, 'ranking': 'harmonic', 'confidence_level': 0.5 - # }}, - # } # transform all vertex indices to their corresponding gene names in a result set for tool in result_sets: