From c86cfaf6e44072da2a12a81e4850bd89de3fe714 Mon Sep 17 00:00:00 2001
From: mlmial <ml.miale@icloud.com>
Date: Mon, 7 Aug 2023 00:03:57 +0200
Subject: [PATCH] made seed variation runable
---
cami_src/cami_suite.py | 23 +++++++++++++++----
.../seed_variation_script.py | 16 +++++++------
2 files changed, 27 insertions(+), 12 deletions(-)
diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py
index 7b33336..2ba4f14 100644
--- a/cami_src/cami_suite.py
+++ b/cami_src/cami_suite.py
@@ -357,14 +357,27 @@ class cami():
for tool in result_sets:
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],
'confidence_level': [0.8],
'ranking': ['trustrank'],
- 'function': {'cami_v3': cami_v3.run_cami}}
-
- cami_setting_list = generate_param_combinations(params_tr)
-
+ 'function': {'cami_v2': cami_v2.run_cami}}
+
+ 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 = {}
for setting in cami_setting_list:
if setting[1]:
diff --git a/cami_src/evaluation_scripts/seed_variation_script.py b/cami_src/evaluation_scripts/seed_variation_script.py
index aecc9cb..3f24ee9 100644
--- a/cami_src/evaluation_scripts/seed_variation_script.py
+++ b/cami_src/evaluation_scripts/seed_variation_script.py
@@ -52,10 +52,12 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
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}')
+ # 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:
+ 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)}
@@ -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]),
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:
+ 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}_{identifier}_relevance_scores.tsv'), 'r') as f:
for line in f:
rel_score = line.split('\t')[1].strip()
res_table.write(f'\t{rel_score}')
@@ -247,4 +249,4 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
fig1.savefig(f'{cami.output_dir}/00_{identifier}_seed_variation_result.png', bbox_inches="tight")
plt.close(fig1)
print(f'Violin plot saved under: 00_{identifier}_seed_variation_result.png')
- return cami
\ No newline at end of file
+ return cami
--
GitLab