Mercurial > repos > mbernt > baseline_toxicity_calculator

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
author mbernt
date Tue, 09 Apr 2024 07:51:18 +0000
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ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
mbernt
parents:
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1 import argparse
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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2 import re
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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4 import pandas as pd
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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6 parser = argparse.ArgumentParser(description='Calculate baseline toxicity for different aquatic species')
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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7 parser.add_argument('--function', type=str, choices=['calculate_baseline', 'apply_linear_functions'],
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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8 help='Function to execute')
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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9 parser.add_argument('--csv_input', type=argparse.FileType('r'), help='Path to the input csv file')
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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10 parser.add_argument('--functions_csv', type=argparse.FileType('r'), default=None,
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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11 help='Path to the csv file containing functions (only for apply_linear_functions)')
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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12 parser.add_argument('--output', type=argparse.FileType('w'), help='Path for the output csv file')
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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13 args = parser.parse_args()
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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15 if args.function == 'calculate_baseline':
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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16 df = pd.read_csv(args.csv_input)
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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17 df.iloc[:, 0] = df.iloc[:, 0].astype(int)
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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18 df['Caenorhabditis elegans [mol/L]'] = 10 ** (-(0.81 * df.iloc[:, 0] + 1.15))
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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19 df['Daphia magna [mol/L]'] = 10 ** (-(0.82 * df.iloc[:, 0] + 1.48))
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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20 df['Danio rerio [mol/L]'] = 10 ** (-(0.99 * df.iloc[:, 0] + 0.78))
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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21 df['Generic Human Cells [mol/L]'] = 0.026 / (10 ** df.iloc[:, 0]) * (1 + 10 ** (0.7 * df.iloc[:, 0] + 0.34) * 3 * 0.001 + 10 ** 3 * 0.07 * 0.001)
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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22 df.to_csv(args.output, index=False)
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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24 elif args.function == 'apply_linear_functions':
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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25 df = pd.read_csv(args.csv_input)
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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26 functions_df = pd.read_csv(args.functions_csv)
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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28 def parse_and_apply_equation(equation, x_values):
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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29 # Extract 'a' and 'b' from the equation (assuming the format 'ax+b' or 'ax-b')
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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30 pattern = re.compile(r'([+-]?\d*\.?\d*)x([+-]\d+)?')
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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31 match = pattern.search(equation)
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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32 a = float(match.group(1)) if match.group(1) not in ('', '+', '-') else 1.0
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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33 b = float(match.group(2)) if match.group(2) else 0
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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34 return a * x_values + b
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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36 for i, row in functions_df.iterrows():
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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37 func = row['function']
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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38 df[f'result_{i}'] = parse_and_apply_equation(func, df['logD'])
ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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39 df.to_csv(args.output, index=False)