Mercurial > repos > recetox > aplcms_to_ramclustr_converter
changeset 2:644192cf22a5 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 5cdd2628a1a509b3e0ccc599eaab63d664bf031a"
| author | recetox |
|---|---|
| date | Wed, 13 Jan 2021 15:55:42 +0000 |
| parents | 52470d439e50 |
| children | 07667688735e |
| files | hdf_converter.py hdf_converter.xml test-data/test-input.h5 test-data/test-output.csv test-data/test.csv test-data/test.h5 |
| diffstat | 6 files changed, 40 insertions(+), 46 deletions(-) [+] |
line wrap: on
line diff
--- a/hdf_converter.py Wed Dec 16 17:28:30 2020 +0000 +++ b/hdf_converter.py Wed Jan 13 15:55:42 2021 +0000 @@ -1,6 +1,6 @@ #!/usr/bin/env python -import optparse +import argparse import sys import warnings @@ -9,55 +9,49 @@ warnings.simplefilter('ignore') -parser = optparse.OptionParser() -parser.add_option("--dataframe", help="Name of hdf dataframe") -parser.add_option("--table", help="Name of a table in the dataframe") -(options, args) = parser.parse_args() +parser = argparse.ArgumentParser() +parser.add_argument("--dataframe", help="Name of hdf dataframe") +parser.add_argument("--table", help="Name of a table in the dataframe") +parser.add_argument('output') +args = parser.parse_args() -def extract_samples(table, num_samples, idx): - intensity_idx = 4 + idx - rt_idx = 4 + num_samples + idx - rt_idx_name = table.columns.tolist()[rt_idx] - table.dropna(subset=[rt_idx_name], inplace=True) - sample_name = table.columns.tolist()[intensity_idx].split('.')[1] - mzrt = table['mz'].map(str) + '_' + table.iloc[:, rt_idx].map(str) - intensity = table.iloc[:, intensity_idx] - mzrt_intensity = {'mz_rt': mzrt, sample_name: intensity} - mzrt_intensity = pd.DataFrame(mzrt_intensity, columns=['mz_rt', sample_name]) - mzrt_intensity.set_index('mz_rt', inplace=True) - return mzrt_intensity +def extract_data(table): + num_samples = int((len(table.columns.tolist()) - 4) / 2) + mz_rt = table['mz'].map(str) + "_" + table['rt'].map(str) + + intensities = table.iloc[:, 4:(4 + num_samples)] + sample_labels = [label.split('.')[1] for label in intensities.columns.tolist()] + ramclustr_data = pd.DataFrame({'mz_rt': mz_rt}) + + for idx in range(num_samples): + label = sample_labels[idx] + ramclustr_data[label] = intensities.iloc[:, idx] + + return ramclustr_data -def join_samples(table): - 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 - RamClustr_data = pd.DataFrame(columns=['mz_rt']) - for sample in range(num_samples): - sample_data = extract_samples(table, num_samples, sample) - RamClustr_data = pd.merge(RamClustr_data, sample_data, on='mz_rt', how='outer') - return RamClustr_data - - -def convert_to_RamClustR(RamClustr_data): - RamClustr_data.fillna(0, inplace=True) - RamClustr_data.rename(columns={'mz_rt': 'sample'}, inplace=True) - RamClustr_data.set_index('sample', inplace=True) - RamClustr_data_transposed = RamClustr_data.transpose() - RamClustr_data_transposed.index.rename('sample', inplace=True) - return RamClustr_data_transposed +def format_table(ramclustr_data): + ramclustr_data.set_index('mz_rt', inplace=True) + ramclustr_data = ramclustr_data.transpose() + ramclustr_data.index.rename('sample', inplace=True) + return ramclustr_data def main(): try: - aplcms_table = pd.read_hdf(options.dataframe, options.table, errors='None') + aplcms_table = pd.read_hdf(args.dataframe, args.table, errors='None') except KeyError: - sys.exit("Selected table does not exist in HDF dataframe") + msg = "Selected table does not exist in HDF dataframe" + print(msg, file=sys.stderr) + sys.exit(1) - RamClustr_data = join_samples(aplcms_table) - RamClustr_data = convert_to_RamClustR(RamClustr_data) - output = args[0] - RamClustr_data.to_csv(output, sep=';') - print("Table '{}' of HDF dataset is converted to csv for RamClutsR".format(options.table)) + ramclustr_data = extract_data(aplcms_table) + ramclustr_table = format_table(ramclustr_data) + + ramclustr_table.to_csv(args.output, sep=',') + msg = "Table '{}' of HDF dataset is converted to csv for RamClutsR".format(args.table) + print(msg, file=sys.stdout) if __name__ == "__main__":
--- a/hdf_converter.xml Wed Dec 16 17:28:30 2020 +0000 +++ b/hdf_converter.xml Wed Jan 13 15:55:42 2021 +0000 @@ -20,9 +20,9 @@ </outputs> <tests> <test> - <param name="hdf_dataframe" value="test.h5" ftype="h5"/> + <param name="hdf_dataframe" value="test-input.h5" ftype="h5"/> <param name="table_name" value="peaks"/> - <output name="out_file" file="test.csv" ftype="csv"/> + <output name="out_file" file="test-output.csv" ftype="csv"/> </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-output.csv Wed Jan 13 15:55:42 2021 +0000 @@ -0,0 +1,4 @@ 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--- a/test-data/test.csv Wed Dec 16 17:28:30 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ 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