From bfb5edd97357ba5b21edabf1e0015f6250343eb6 Mon Sep 17 00:00:00 2001
From: Schneider Leo <leo.schneider@etu.ec-lyon.fr>
Date: Fri, 20 Sep 2024 11:41:29 +0200
Subject: [PATCH] typo
---
.idea/misc.xml | 2 +-
common_dataset.py | 2 +-
data_viz.py | 9 ++++-----
main_custom.py | 2 +-
requirements.txt | 2 +-
5 files changed, 8 insertions(+), 9 deletions(-)
diff --git a/.idea/misc.xml b/.idea/misc.xml
index 1b5f6f7..cde01ce 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -3,5 +3,5 @@
<component name="Black">
<option name="sdkName" value="Python 3.9 (LC-MS-RT-prediction)" />
</component>
- <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.9 (LC-MS-RT-prediction)" project-jdk-type="Python SDK" />
+ <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.11 (LC-MS-RT-prediction)" project-jdk-type="Python SDK" />
</project>
\ No newline at end of file
diff --git a/common_dataset.py b/common_dataset.py
index 5ab8a5f..6e46845 100644
--- a/common_dataset.py
+++ b/common_dataset.py
@@ -95,7 +95,7 @@ def alphabetical_to_numerical(seq, vocab):
else :
for i in range(len(seq) - 2 * seq.count('-')):
if seq[i + dec] != '-':
- num.append(ALPHABET_UNMOD[seq[i + dec]])
+ num.append(IUPAC_VOCAB[seq[i + dec]])
else:
if seq[i + dec + 1:i + dec + 4] == 'CaC':
num.append(21)
diff --git a/data_viz.py b/data_viz.py
index 3d0f590..23dec3e 100644
--- a/data_viz.py
+++ b/data_viz.py
@@ -1,10 +1,9 @@
-from unittest.mock import inplace
import matplotlib.pyplot as plt
import numpy as np
import random
import pandas as pd
-from sympy.utilities.misc import replace
+
from mass_prediction import compute_frag_mz_ration
@@ -230,9 +229,9 @@ def add_length(dataframe):
dataframe['length']=dataframe['seq'].map(fonc)
-df = pd.read_csv('output/out_ISA.csv')
+df = pd.read_csv('output/out_ISA_no_tape.csv')
add_length(df)
df['abs_error'] = np.abs(df['rt pred']-df['true rt'])
-# histo_abs_error(df, display=False, save=True, path='temp.png')
-scatter_rt(df, display=False, save=True, path='temp.png')
+histo_abs_error(df, display=False, save=True, path='temp.png')
+# scatter_rt(df, display=False, save=True, path='temp.png')
# histo_length_by_error(df, 10, save=True, path='temp.png')
\ No newline at end of file
diff --git a/main_custom.py b/main_custom.py
index fcc9074..ea21899 100644
--- a/main_custom.py
+++ b/main_custom.py
@@ -202,7 +202,7 @@ def main(args):
path_test=args.dataset_test,
batch_size=args.batch_size, length=25, pad = False, convert=True, vocab='iapuc')
elif args.forward == 'rt':
- data_train, data_val, data_test = dataloader.load_data(data_source=args.dataset_train,
+ data_train, data_val, data_test = dataloader.load_data(data_sources=args.dataset_train,
batch_size=args.batch_size, length=25)
print('\nData loaded')
diff --git a/requirements.txt b/requirements.txt
index 14fc58a..7d0c671 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -13,7 +13,7 @@ scikit-learn~=1.4.1.post1
Levenshtein~=0.25.0
keras~=2.15.0
tensorflow~=2.15.0.post1
-pillow~=10.1.0
+pillow~=10.3.0
nibabel~=5.2.1
nilearn~=0.10.4
scipy~=1.12.0
--
GitLab