Mercurial > repos > recetox > aplcms_to_ramclustr_converter

comparison hdf_converter.py @ 1:52470d439e50 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 9a479980d3432f6f1a4541bac75b4ccc40d189ee"
author recetox
date Wed, 16 Dec 2020 17:28:30 +0000
parents 062f4c571a24
children 644192cf22a5
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0:062f4c571a24 1:52470d439e50
51 try: 51 try:
52 aplcms_table = pd.read_hdf(options.dataframe, options.table, errors='None') 52 aplcms_table = pd.read_hdf(options.dataframe, options.table, errors='None')
53 except KeyError: 53 except KeyError:
54 sys.exit("Selected table does not exist in HDF dataframe") 54 sys.exit("Selected table does not exist in HDF dataframe")
55 55
56 RamClutsr_data = join_samples(aplcms_table) 56 RamClustr_data = join_samples(aplcms_table)
57 RamClustr_data = convert_to_RamClustR(RamClutsr_data) 57 RamClustr_data = convert_to_RamClustR(RamClustr_data)
58 output = args[0] 58 output = args[0]
59 RamClustr_data.to_csv(output, sep=';') 59 RamClustr_data.to_csv(output, sep=';')
60 print("Table '{}' of HDF dataset is converted to csv for RamClutsR".format(options.table)) 60 print("Table '{}' of HDF dataset is converted to csv for RamClutsR".format(options.table))
61 61
62 62