--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hdf_converter.py	Tue Dec 15 17:38:07 2020 +0000
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+
+import optparse
+import sys
+import warnings
+
+import pandas as pd
+
+
+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()
+
+
+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 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 main():
+    try:
+        aplcms_table = pd.read_hdf(options.dataframe, options.table, errors='None')
+    except KeyError:
+        sys.exit("Selected table does not exist in HDF dataframe")
+
+    RamClutsr_data = join_samples(aplcms_table)
+    RamClustr_data = convert_to_RamClustR(RamClutsr_data)
+    output = args[0]
+    RamClustr_data.to_csv(output, sep=';')
+    print("Table '{}' of HDF dataset is converted to csv for RamClutsR".format(options.table))
+
+
+if __name__ == "__main__":
+    main()