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b/tests/test_disease.py |
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from openomics.database.disease import DisGeNet, LncRNADisease, HMDD, MalaCards |
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from .test_multiomics import * |
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@pytest.fixture |
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def generate_DisGeNet_ftp(): |
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return DisGeNet(path="https://www.disgenet.org/static/disgenet_ap1/files/downloads/", curated=True) |
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@pytest.fixture |
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def generate_LncRNADisease_ftp(): |
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return LncRNADisease(path="http://www.cuilab.cn/files/images/ldd/", species="Human") |
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@pytest.fixture |
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def generate_HMDD_ftp(): |
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return HMDD(path="http://www.cuilab.cn/static/hmdd3/data/") |
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@pytest.fixture |
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def generate_MalaCards_ftp(): |
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return MalaCards() |
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def test_import_DisGeNet(generate_DisGeNet_ftp): |
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""" |
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Args: |
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generate_DisGeNet_ftp: |
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""" |
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assert generate_DisGeNet_ftp.data_path == "https://www.disgenet.org/static/disgenet_ap1/files/downloads/" |
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assert not generate_DisGeNet_ftp.get_disease_assocs(index="gene_name").empty |
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def test_annotate_DisGeNet(generate_TCGA_LUAD, generate_DisGeNet_ftp): |
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""" |
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Args: |
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generate_TCGA_LUAD: |
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generate_DisGeNet_ftp: |
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""" |
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generate_TCGA_LUAD.MessengerRNA.annotate_diseases(generate_DisGeNet_ftp, on="gene_name", ) |
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assert {'disease_associations'}.issubset(generate_TCGA_LUAD.MessengerRNA.annotations.columns) |
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def test_import_HMDD(generate_HMDD_ftp): |
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""" |
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Args: |
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generate_HMDD_ftp: |
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""" |
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assert generate_HMDD_ftp.data_path == "http://www.cuilab.cn/static/hmdd3/data/" |
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assert not generate_HMDD_ftp.get_disease_assocs(index="gene_name").empty |
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def test_annotate_HMDD(generate_TCGA_LUAD, generate_HMDD_ftp): |
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""" |
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Args: |
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generate_TCGA_LUAD: |
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generate_HMDD_ftp: |
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""" |
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generate_TCGA_LUAD.MicroRNA.annotate_diseases(generate_HMDD_ftp, on="gene_name", ) |
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assert {'disease_associations'}.issubset(generate_TCGA_LUAD.MicroRNA.annotations.columns) |
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def test_LncRNADisease(generate_LncRNADisease_ftp): |
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""" |
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Args: |
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generate_LncRNADisease_ftp: |
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""" |
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assert generate_LncRNADisease_ftp.data_path == "http://www.cuilab.cn/files/images/ldd/" |
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assert not generate_LncRNADisease_ftp.get_disease_assocs(index="gene_name").empty |
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def test_annotate_LncRNADisease(generate_TCGA_LUAD, generate_LncRNADisease_ftp): |
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""" |
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Args: |
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generate_TCGA_LUAD: |
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generate_LncRNADisease_ftp: |
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""" |
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generate_TCGA_LUAD.LncRNA.annotate_diseases(generate_LncRNADisease_ftp, on="gene_name", ) |
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assert {'disease_associations'}.issubset(generate_TCGA_LUAD.LncRNA.annotations.columns) |
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def test_import_MalaCards(generate_MalaCards_ftp): |
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""" |
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Args: |
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generate_MalaCards_ftp: |
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""" |
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assert generate_MalaCards_ftp.data_path == "http://zdzlab.einstein.yu.edu/1/hedd/" |