From b55e698e1198c12602ad0d0899efbef43e55abd6 Mon Sep 17 00:00:00 2001
From: Schneider Leo <leo.schneider@etu.ec-lyon.fr>
Date: Wed, 23 Oct 2024 13:11:38 +0200
Subject: [PATCH] datasets

---
 alignement.py                      |     16 +-
 data_viz.py                        |     10 +-
 database/data_ISA_augmented_10.csv | 137545 ++++++++++++++++++++++++++
 database/data_ISA_augmented_5.csv  | 107727 ++++++++++++++++++++
 database/data_ISA_augmented_7.csv  | 120591 ++++++++++++++++++++++
 5 files changed, 365876 insertions(+), 13 deletions(-)
 create mode 100644 database/data_ISA_augmented_10.csv
 create mode 100644 database/data_ISA_augmented_5.csv
 create mode 100644 database/data_ISA_augmented_7.csv

diff --git a/alignement.py b/alignement.py
index de60fb1..969e06e 100644
--- a/alignement.py
+++ b/alignement.py
@@ -211,36 +211,36 @@ def compare_include_df(df, sub_df, save = True, path = 'temp.png'):
 
 
 # create augmented dataset from ISA data + column invariant prosit peptides
-df_base = pd.read_pickle('database/data_ISA_dual_align_train.pkl')
+df_base = pd.read_pickle('database/data_DIA_ISA_55_train.pkl')
 df_base = df_base[['Sequence','Retention time']]
 
-df_1 = pd.read_pickle('database/data_prosit_threshold_1.pkl')
+df_1 = pd.read_pickle('database/data_prosit_threshold_5.pkl')
 df_1['Sequence']= df_1['Sequence'].map(numerical_to_alphabetical_str)
 
-df_2 = pd.read_pickle('database/data_prosit_threshold_2.pkl')
+df_2 = pd.read_pickle('database/data_prosit_threshold_7.pkl')
 df_2['Sequence']= df_2['Sequence'].map(numerical_to_alphabetical_str)
 
-df_3 = pd.read_pickle('database/data_prosit_threshold_3.pkl')
+df_3 = pd.read_pickle('database/data_prosit_threshold_10.pkl')
 df_3['Sequence']= df_3['Sequence'].map(numerical_to_alphabetical_str)
 
 df_augmented_1 = pd.concat([df_1,df_base],axis=0).reset_index(drop=True)
 df_augmented_1.columns=['sequence','irt']
 df_augmented_1['state']='train'
-df_augmented_1.to_csv('database/data_ISA_augmented_1_30_01.csv')
+df_augmented_1.to_csv('database/data_ISA_augmented_5.csv')
 
 df_augmented_2 = pd.concat([df_2,df_base],axis=0).reset_index(drop=True)
 df_augmented_2.columns=['sequence','irt']
 df_augmented_2['state']='train'
-df_augmented_2.to_csv('database/data_ISA_augmented_2_30_01.csv')
+df_augmented_2.to_csv('database/data_ISA_augmented_7.csv')
 
 df_augmented_3 = pd.concat([df_3,df_base],axis=0).reset_index(drop=True)
 df_augmented_3.columns=['sequence','irt']
 df_augmented_3['state']='train'
-df_augmented_3.to_csv('database/data_ISA_augmented_3_30_01.csv')
+df_augmented_3.to_csv('database/data_ISA_augmented_10.csv')
 
 
 # testing intersection between test and augmented dataset
-df_sup = pd.read_pickle('database/data_prosit_threshold_3.pkl')
+df_sup = pd.read_pickle('database/data_prosit_threshold_10.pkl')
 df_test = pd.read_pickle('database/data_DIA_ISA_55_test.pkl')
 
 inter = []
diff --git a/data_viz.py b/data_viz.py
index a9060d0..32990e7 100644
--- a/data_viz.py
+++ b/data_viz.py
@@ -308,10 +308,10 @@ scatter_rt(df, display=False, save=True, path='fig/custom model res/RT_pred_ISA_
 
 ## Compare error variation between run
 ## Prosit column changes affect some peptides more than others (but consistently)
-# df_1 = pd.read_csv('output/out_common_ISA_prosit_eval.csv')
-# df_2 = pd.read_csv('output/out_common_ISA_prosit_eval_2.csv')
-#
-# df = select_best_data(df_1, df_2, 3)
-# df.to_pickle('database/data_prosit_threshold_3.pkl')
+df_1 = pd.read_csv('output/out_common_ISA_prosit_eval.csv')
+df_2 = pd.read_csv('output/out_common_ISA_prosit_eval_2.csv')
+
+df = select_best_data(df_1, df_2, 7)
+df.to_pickle('database/data_prosit_threshold_7.pkl')
 # compare_error(df_1,df_2,save=True,path='fig/custom model res/ISA_prosit_error_variation.png')
 
diff --git a/database/data_ISA_augmented_10.csv b/database/data_ISA_augmented_10.csv
new file mode 100644
index 0000000..63bbc78
--- /dev/null
+++ b/database/data_ISA_augmented_10.csv
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