diff --git a/.idea/misc.xml b/.idea/misc.xml index 1b5f6f736536803396a9f042bfdc1981e5153ac8..cde01ce4f1c28496b5ffbb181b9aa0e7b9db0fda 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 5ab8a5f21583168a1371968847032ef911f2f156..6e468458a2e17c03a65e851ece6db955df3f9bb6 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 3d0f590b2006daec7cc598eb6a84494fe004d2d4..23dec3e3ab745a476cf7b2281d59fccab93d8d54 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 fcc907494f8c2419cfd47376f0c5a9f4fac3a94c..ea218998d1c57ad39189898d949f0e52208349ec 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 14fc58aa246bd3bd6bcef78ab5ced90da2fa0734..7d0c671229d57f0969da758d16b229d92ce5764c 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