From 5da128cc92fb4ab3e6ae8688af9d4bd6da490f59 Mon Sep 17 00:00:00 2001
From: bay9355 <mia.le@studium.uni-hamburg.de>
Date: Thu, 13 Apr 2023 21:46:02 +0200
Subject: [PATCH] added functional relevance to seed_var result table
---
cami_src/cami_suite.py | 50 +++++++++++--------
.../seed_variation_script.py | 11 ++++
2 files changed, 40 insertions(+), 21 deletions(-)
diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py
index c7554d2..e1ed51a 100644
--- a/cami_src/cami_suite.py
+++ b/cami_src/cami_suite.py
@@ -239,27 +239,35 @@ class cami():
prefix=f'{result_set}_{self.uid}',
file_type='png')
- sub_validation_results = biodigest.single_validation.single_validation(
- tar=set(self.result_module_sets[result_set]),
- tar_id='entrez',
- mode='subnetwork-set',
- distance='jaccard',
- network_data={"network_file":ppi_graph_file,
- "prop_name":"name",
- "id_type":"entrez"},
- ref=set(seed_gene_lst),
- ref_id='entrez'
- )
- if sub_validation_results['status'] == 'ok':
- biodigest.single_validation.save_results(sub_validation_results, f'{result_set}_{self.uid}',
- self.output_dir)
- biodigest.evaluation.d_utils.plotting_utils.create_plots(results=sub_validation_results,
- mode='subnetwork-set',
- tar=set(self.result_module_sets[result_set]),
- tar_id='entrez',
- out_dir=self.output_dir,
- prefix=f'{result_set}_{self.uid}',
- file_type='png')
+ with open(os.path.join(self.tmp_dir, f'{result_set}_{self.uid}_relevance_scores.tsv'), 'w') as f:
+ rel_score_name = list(set_validation_results['input_values']['values'].keys())[0]
+ f.write(f'value\t{rel_score_name}\n')
+ val_res_dct = set_validation_results['input_values']['values'][rel_score_name]
+ for val in val_res_dct:
+ f.write(f'{val}\t{val_res_dct[val]}\n')
+
+ # sub_validation_results = biodigest.single_validation.single_validation(
+ # tar=set(self.result_module_sets[result_set]),
+ # tar_id='entrez',
+ # mode='subnetwork-set',
+ # distance='jaccard',
+ # network_data={"network_file":ppi_graph_file,
+ # "prop_name":"name",
+ # "id_type":"entrez"},
+ # ref=set(seed_gene_lst),
+ # ref_id='entrez'
+ # )
+ # if sub_validation_results['status'] == 'ok':
+ # biodigest.single_validation.save_results(sub_validation_results, f'{result_set}_{self.uid}',
+ # self.output_dir)
+ # biodigest.evaluation.d_utils.plotting_utils.create_plots(results=sub_validation_results,
+ # mode='subnetwork-set',
+ # tar=set(self.result_module_sets[result_set]),
+ # tar_id='entrez',
+ # out_dir=self.output_dir,
+ # prefix=f'{result_set}_{self.uid}',
+ # file_type='png')
+
def run_threaded_tool(self, tool, pred_sets):
"""run a tool in one thread and save the results into a dictionary pred_sets
diff --git a/cami_src/evaluation_scripts/seed_variation_script.py b/cami_src/evaluation_scripts/seed_variation_script.py
index 7724205..aecc9cb 100644
--- a/cami_src/evaluation_scripts/seed_variation_script.py
+++ b/cami_src/evaluation_scripts/seed_variation_script.py
@@ -51,6 +51,11 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
res_table.write(f'\t{tool}_rdr_ks_pvalue')
for tool in prediction_tools:
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:
+ for line in f:
+ val_name = line.split('\t')[0]
+ redisc_table.write(f'\t{val_name}')
res_table.write('\n')
# result dictionaries of the form {tool:list(value for each iteration)}
@@ -135,6 +140,12 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
for pred_tool in prediction_tools:
p_val = kolmogorov_smirnoff.calculate_ks_p_value(list(module_size_dict[tool]),
list(module_size_dict[pred_tool]))
+ res_table.write(f'\t{p_val}')
+
+ with open(os.path.join(cami.tmp_dir, f'{tool}_{cami.uid}_relevance_scores.tsv)'), 'r') as f:
+ for line in f:
+ rel_score = line.split('\t')[1].strip()
+ res_table.write(f'\t{rel_score}')
res_table.write('\n')
print(f'Result tables are saved in the following locations:')
--
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