From b0c61843668682cc53e77801bce4c42708cf7ea3 Mon Sep 17 00:00:00 2001
From: bay9355 <mia.le@studium.uni-hamburg.de>
Date: Mon, 3 Apr 2023 18:41:59 +0200
Subject: [PATCH] edited cami_suite
---
cami_src/cami_suite.py | 32 ++++++++++++++++++++++++--------
1 file changed, 24 insertions(+), 8 deletions(-)
diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py
index 3d79bad..599be5a 100644
--- a/cami_src/cami_suite.py
+++ b/cami_src/cami_suite.py
@@ -14,6 +14,15 @@ import itertools
def generate_param_combinations(params_dict):
+ """
+ Generates all possible combinations of parameters for the given function(s) and returns them as a list.
+
+ Args:
+ params_dict (dict): A dictionary containing the parameters and their possible values for each function.
+
+ Returns:
+ list: A list of lists where each inner list contains the function name, parameter string, and a dictionary with the parameter values and corresponding function.
+ """
params_keys = list(params_dict.keys())
params_values = [params_dict[k] for k in params_keys if k != 'function']
function_dict = params_dict['function']
@@ -110,6 +119,7 @@ class cami():
self.seed_lst = seed_lst
self.origin_seed_lst = seed_lst.copy()
self.tool_wrappers = tool_wrappers
+ self.prediction_tools = [wrapper.name for wrapper in tool_wrappers]
self.toolweights = toolweights
self.home_path = home_path
if uid==None:
@@ -347,18 +357,24 @@ class cami():
'first_neighbours': cami_v1.make_first_neighbor_result_set}
}
- params_tr = {'hub_penalty': [0, 0.25, 0.5, 0.75, 1.0],
- 'damping_factor': [0.1, 0.25, 0.5, 0.75],
- 'confidence_level': [0.2, 0.35, 0.5, 0.75],
+ params_tr = {'hub_penalty': [0.5],
+ 'damping_factor': [0.5],
+ '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, 0.25, 0.5, 0.75, 1.0],
- 'confidence_level': [0.2, 0.35, 0.5, 0.75],
+ 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}}
+ '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}}
c = generate_param_combinations(params_0)
cami_setting_list = generate_param_combinations(params_0)+\
@@ -369,7 +385,7 @@ class cami():
camis = {}
for setting in cami_setting_list:
if setting[1]:
- func_name = setting[0] + '_' +setting[1]
+ func_name = setting[0] + '_' +setting[1].rsplit('_', 1)[-1]
else:
func_name = setting[0]
@@ -553,7 +569,7 @@ class cami():
else:
print('Cannot use degradome to create venn diagrams of 6 or more tools')
return None
-
+
def download_diagram(self, url):
venn_name = f'{self.output_dir}/vdiagram_{self.uid}'
response = degradome.download_image(url, venn_name + '.png')
--
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