Mercurial > repos > bgruening > flexynesis_plot

annotate index_to_name.py @ 6:a9d1fe48e1e6 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit bcee55468e70cd025cc5359bef5e9991e893eca9
author bgruening
date Thu, 16 Oct 2025 20:16:03 +0000
parents 07f595f34f29
children
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents:
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1 #!/usr/bin/env python
07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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3 import sys
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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4 from pathlib import Path
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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6 import pandas as pd
07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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9 def get_column_names(file_path, indices):
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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10 """
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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11 Get column names based on multiple indices from a tabular file.
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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12 """
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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13 try:
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 4
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14 file_ext = Path(file_path).suffix.lower()
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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15 sep = ',' if file_ext == '.csv' else '\t'
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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17 if file_ext in ['.csv', '.tsv', '.txt', '.tab', '.tabular']:
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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18 data = pd.read_csv(file_path, sep=sep)
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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19 else:
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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20 raise ValueError(f"Unsupported file extension: {file_ext}")
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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22 except Exception as e:
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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23 raise ValueError(f"Error loading data from {file_path}: {e}") from e
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 4
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25 column_names = []
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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27 for index in indices:
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 4
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28 zero_based_index = index - 1 # Convert to zero-based index
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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29 if zero_based_index < 0 or zero_based_index >= len(data.columns):
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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30 print(f"Error: Index {index} is out of range. File has {len(data.columns)} columns (1-{len(data.columns)}).")
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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31 return None
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 4
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32 column_names.append(data.columns[zero_based_index].strip())
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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34 return column_names
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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37 if __name__ == "__main__":
07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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39 file_path = sys.argv[1]
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 4
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40 indices_str = sys.argv[2]
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07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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42 # Parse comma-separated indices
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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43 try:
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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44 indices = [int(i.strip()) for i in indices_str.split(',')]
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 4
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45 except ValueError:
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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46 print("Error: All indices must be integers.")
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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47 sys.exit(1)
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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49 result = get_column_names(file_path, indices)
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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50 if result is not None:
07f595f34f29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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51 print(','.join(result))