--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aplcms_to_ramclustr_converter.py	Wed Feb 17 15:14:33 2021 +0000
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+import argparse
+import sys
+import warnings
+
+import pandas as pd
+
+
+warnings.simplefilter('ignore')
+
+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_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 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(args.dataframe, args.table, errors='None')
+    except KeyError:
+        msg = "Selected table does not exist in HDF dataframe"
+        print(msg, file=sys.stderr)
+        sys.exit(1)
+
+    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__":
+    main()