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"""_resultsTest writing GOATOOLS Gene Ontology Gene Enrichment results to a Python module.""" |
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import os |
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import importlib |
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from goatools.test_data.nature3102_goea import get_goea_results |
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from goatools.nt_utils import wr_py_nts |
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from goatools.rpt.goea_nt_xfrm import get_goea_nts_prt |
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def test_wrpy(): |
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"""Test writing GOATOOLS GOEA results to a Python module as a list of nts.""" |
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# 1. Run GOATOOLS Gene Ontology Enrichment Analysis |
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nature_data = get_goea_results() |
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# 2. Convert GOATOOLS GOEA results into a list of namedtuples |
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goea_results = nature_data['goea_results'] |
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nts_goea = get_goea_nts_prt(goea_results) |
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# 3. Save GOATOOLS GOEA into a Python module |
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# 3a. Python module name |
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module_name = "nbt3102_goea" |
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fout_py = get_fout_py(module_name) |
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# 3b. Save GOATOOLS GOEA into a Python module |
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wr_py_nts(fout_py, nts_goea, varname="nts") |
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# 4. Check results |
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nts_py = importlib.import_module(module_name).nts |
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assert len(nts_goea) == len(nts_py) |
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# Alternatively, save module through goea object |
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module_name = "nbt3102_goea_alt" |
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fout_py = get_fout_py(module_name) |
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nature_data['goeaobj'].wr_py_goea_results(fout_py, goea_results) |
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nts_py = importlib.import_module(module_name).goea_results |
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assert len(nts_goea) == len(nts_py) |
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def get_fout_py(module_name): |
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"""Given a module name, return the name of the corresponding Python file.""" |
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fout_py = "{MODULE}.py".format(MODULE=module_name) |
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if os.path.isfile(fout_py): |
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os.remove(fout_py) |
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return fout_py |
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if __name__ == '__main__': |
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test_wrpy() |
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tanghaibao /
goatools
