Mercurial > repos > recetox > aplcms_to_ramclustr_converter

annotate aplcms_to_ramclustr_converter.py @ 3:07667688735e draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
author recetox
date Wed, 17 Feb 2021 15:14:33 +0000
parents
children 9ea34e24474f
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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1 #!/usr/bin/env python
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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3 import argparse
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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4 import sys
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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5 import warnings
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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7 import pandas as pd
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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10 warnings.simplefilter('ignore')
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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12 parser = argparse.ArgumentParser()
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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13 parser.add_argument("--dataframe", help="Name of hdf dataframe")
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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14 parser.add_argument("--table", help="Name of a table in the dataframe")
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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15 parser.add_argument('output')
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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16 args = parser.parse_args()
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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19 def extract_data(table):
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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20 num_samples = int((len(table.columns.tolist()) - 4) / 2)
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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21 mz_rt = table['mz'].map(str) + "_" + table['rt'].map(str)
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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23 intensities = table.iloc[:, 4:(4 + num_samples)]
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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24 sample_labels = [label.split('.')[1] for label in intensities.columns.tolist()]
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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25 ramclustr_data = pd.DataFrame({'mz_rt': mz_rt})
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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27 for idx in range(num_samples):
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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28 label = sample_labels[idx]
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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29 ramclustr_data[label] = intensities.iloc[:, idx]
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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31 return ramclustr_data
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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34 def format_table(ramclustr_data):
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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35 ramclustr_data.set_index('mz_rt', inplace=True)
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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36 ramclustr_data = ramclustr_data.transpose()
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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37 ramclustr_data.index.rename('sample', inplace=True)
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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38 return ramclustr_data
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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41 def main():
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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42 try:
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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43 aplcms_table = pd.read_hdf(args.dataframe, args.table, errors='None')
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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44 except KeyError:
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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45 msg = "Selected table does not exist in HDF dataframe"
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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46 print(msg, file=sys.stderr)
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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47 sys.exit(1)
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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49 ramclustr_data = extract_data(aplcms_table)
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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50 ramclustr_table = format_table(ramclustr_data)
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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52 ramclustr_table.to_csv(args.output, sep=',')
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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53 msg = "Table '{}' of HDF dataset is converted to csv for RamClutsR".format(args.table)
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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54 print(msg, file=sys.stdout)
07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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07667688735e "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
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57 if __name__ == "__main__":
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58 main()