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Commit c86cfaf6 authored by mlmial's avatar mlmial
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made seed variation runable

parent 2518dde2
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...@@ -357,13 +357,26 @@ class cami(): ...@@ -357,13 +357,26 @@ class cami():
for tool in result_sets: for tool in result_sets:
result_sets[tool] -= set(self.seed_lst) result_sets[tool] -= set(self.seed_lst)
params_tr = {'hub_penalty': [0.25], params_0 = {'function': {'union':cami_v1.make_union,
'intersection':cami_v1.make_intersection,
'first_neighbours': cami_v1.make_first_neighbor_result_set}
}
params_tr1 = {'hub_penalty': [0.5],
'damping_factor': [0.75], 'damping_factor': [0.75],
'confidence_level': [0.8], 'confidence_level': [0.8],
'ranking': ['trustrank'], 'ranking': ['trustrank'],
'function': {'cami_v3': cami_v3.run_cami}} 'function': {'cami_v2': cami_v2.run_cami}}
cami_setting_list = generate_param_combinations(params_tr) params_tr2 = {'hub_penalty': [0.5],
'damping_factor': [0.85],
'confidence_level': [0.65],
'ranking': ['trustrank'],
'function': {'cami_v3': cami_v3.run_cami}
}
cami_setting_list = generate_param_combinations(params_0)+\
generate_param_combinations(params_tr1)+\
generate_param_combinations(params_tr2)
camis = {} camis = {}
for setting in cami_setting_list: for setting in cami_setting_list:
......
...@@ -52,7 +52,9 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru ...@@ -52,7 +52,9 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
for tool in prediction_tools: for tool in prediction_tools:
res_table.write(f'\t{tool}_msr_ks_pvalue') res_table.write(f'\t{tool}_msr_ks_pvalue')
with open(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{cami.uid}_relevance_scores.tsv)'), 'r') as f: # if relevance scores file exsits:
if os.path.exists(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{identifier}_relevance_scores.tsv)')):
with open(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{identifier}_relevance_scores.tsv)'), 'r') as f:
for line in f: for line in f:
val_name = line.split('\t')[0] val_name = line.split('\t')[0]
redisc_table.write(f'\t{val_name}') redisc_table.write(f'\t{val_name}')
...@@ -141,8 +143,8 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru ...@@ -141,8 +143,8 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
p_val = kolmogorov_smirnoff.calculate_ks_p_value(list(module_size_dict[tool]), p_val = kolmogorov_smirnoff.calculate_ks_p_value(list(module_size_dict[tool]),
list(module_size_dict[pred_tool])) list(module_size_dict[pred_tool]))
res_table.write(f'\t{p_val}') res_table.write(f'\t{p_val}')
if os.path.exists(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{identifier}_relevance_scores.tsv)')):
with open(os.path.join(cami.tmp_dir, f'{tool}_{cami.uid}_relevance_scores.tsv)'), 'r') as f: with open(os.path.join(cami.tmp_dir, f'{tool}_{identifier}_relevance_scores.tsv'), 'r') as f:
for line in f: for line in f:
rel_score = line.split('\t')[1].strip() rel_score = line.split('\t')[1].strip()
res_table.write(f'\t{rel_score}') res_table.write(f'\t{rel_score}')
......
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