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"""tests/test_dnlds.py: Test downloading go-basic.obo file and goslims obo/owl.""" |
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import os |
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import sys |
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from goatools.base import download_go_basic_obo |
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from goatools.base import download_ncbi_associations |
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def test_dnlds(prt=sys.stdout): |
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"""Test downloads of ontologies and NCBI associations.""" |
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goslims = [ |
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'goslim_aspergillus', |
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'goslim_candida', |
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#'goslim_chembl', # 404 not found |
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'goslim_generic', |
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'goslim_metagenomics', |
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'goslim_pir', |
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'goslim_plant', |
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'goslim_pombe', |
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'goslim_synapse', |
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'goslim_virus', |
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'goslim_yeast'] |
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# Test downloads of ontologies. |
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cwd = os.getcwd() |
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dnld_ontology(os.path.join(cwd, "go-basic.obo")) |
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# Test downloads of go-slim ontologies. |
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for goslim in goslims: |
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for ext in ['obo', 'owl']: |
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file_dst = os.path.join(cwd, "{DAG}.{EXT}".format(DAG=goslim, EXT=ext)) |
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dnld_ontology(file_dst) |
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# Test downloading of associations from NCBI. |
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file_assc = os.path.join(cwd, "gene2go") |
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#os.system("rm -f {FILE}".format(FILE=file_assc)) |
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#download_ncbi_associations(file_assc, prt, loading_bar=None) |
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#download_ncbi_associations(file_assc, prt, loading_bar=None) |
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#assert os.path.isfile(file_assc), "FILE({F}) EXPECTED TO EXIST".format(F=file_assc) |
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def dnld_ontology(filename): |
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"""Test downloading of ontologies.""" |
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# download_go_basic_obo(filename, loading_bar=None) |
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os.system("rm -f {FILE}".format(FILE=filename)) |
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download_go_basic_obo(filename, loading_bar=None) |
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download_go_basic_obo(filename, loading_bar=None) |
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assert os.path.isfile(filename), "FILE({F}) EXPECTED TO EXIST".format(F=filename) |
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if __name__ == '__main__': |
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test_dnlds() |
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tanghaibao /
goatools
