Mercurial > repos > recetox > aplcms_to_ramclustr_converter

annotate hdf_converter.py @ 0:062f4c571a24 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
author recetox
date Tue, 15 Dec 2020 17:38:07 +0000
parents
children 52470d439e50
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062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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1 #!/usr/bin/env python
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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3 import optparse
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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4 import sys
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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5 import warnings
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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7 import pandas as pd
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10 warnings.simplefilter('ignore')
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12 parser = optparse.OptionParser()
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13 parser.add_option("--dataframe", help="Name of hdf dataframe")
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14 parser.add_option("--table", help="Name of a table in the dataframe")
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15 (options, args) = parser.parse_args()
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18 def extract_samples(table, num_samples, idx):
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19 intensity_idx = 4 + idx
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20 rt_idx = 4 + num_samples + idx
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21 rt_idx_name = table.columns.tolist()[rt_idx]
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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22 table.dropna(subset=[rt_idx_name], inplace=True)
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23 sample_name = table.columns.tolist()[intensity_idx].split('.')[1]
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24 mzrt = table['mz'].map(str) + '_' + table.iloc[:, rt_idx].map(str)
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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25 intensity = table.iloc[:, intensity_idx]
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26 mzrt_intensity = {'mz_rt': mzrt, sample_name: intensity}
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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27 mzrt_intensity = pd.DataFrame(mzrt_intensity, columns=['mz_rt', sample_name])
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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28 mzrt_intensity.set_index('mz_rt', inplace=True)
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29 return mzrt_intensity
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32 def join_samples(table):
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33 num_samples = int((len(table.columns.tolist()) - 4) / 2) # 4 default columns: mz,rt,mz_min,mz_max. The rest is intensity and rt columns for each sample
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34 RamClustr_data = pd.DataFrame(columns=['mz_rt'])
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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35 for sample in range(num_samples):
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36 sample_data = extract_samples(table, num_samples, sample)
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37 RamClustr_data = pd.merge(RamClustr_data, sample_data, on='mz_rt', how='outer')
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38 return RamClustr_data
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41 def convert_to_RamClustR(RamClustr_data):
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42 RamClustr_data.fillna(0, inplace=True)
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43 RamClustr_data.rename(columns={'mz_rt': 'sample'}, inplace=True)
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44 RamClustr_data.set_index('sample', inplace=True)
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45 RamClustr_data_transposed = RamClustr_data.transpose()
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46 RamClustr_data_transposed.index.rename('sample', inplace=True)
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47 return RamClustr_data_transposed
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50 def main():
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51 try:
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52 aplcms_table = pd.read_hdf(options.dataframe, options.table, errors='None')
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53 except KeyError:
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54 sys.exit("Selected table does not exist in HDF dataframe")
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56 RamClutsr_data = join_samples(aplcms_table)
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57 RamClustr_data = convert_to_RamClustR(RamClutsr_data)
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58 output = args[0]
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59 RamClustr_data.to_csv(output, sep=';')
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60 print("Table '{}' of HDF dataset is converted to csv for RamClutsR".format(options.table))
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63 if __name__ == "__main__":
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64 main()