--- a +++ b/tests/test_interaction.py @@ -0,0 +1,64 @@ +from openomics.database.interaction import LncRNA2Target, STRING, MiRTarBase + +from .test_multiomics import * + +# FIXME: URL is broken. Can't find a link to this database. +# @pytest.fixture +# def generate_LncRNA2Target(): +# return LncRNA2Target(path="http://123.59.132.21/lncrna2target/data/", version="low_throughput") + + +# def test_import_LncRNA2Target(generate_LncRNA2Target): +# """ +# Args: +# generate_LncRNA2Target: +# """ +# assert generate_LncRNA2Target.data_path is not None + + +@pytest.fixture +def generate_STRING(): + string = STRING(edge_attr=["weight"], index_col=0) + string.data = string.data.sample(frac=0.01) + return string + + +@pytest.fixture +def generate_MiRTarBase(): + return MiRTarBase( + path="/data/datasets/Bioinformatics_ExternalData/miRTarBase/", # Hard-coded + strip_mirna_name=True, + filters={"Species (Target Gene)": "Homo sapiens"}) + + +# Test disabled since obtaining MiRTarBase via ftp is unreachable +# def test_import_MiRTarBase(generate_MiRTarBase): +# """ +# Args: +# generate_MiRTarBase: +# """ +# assert generate_MiRTarBase.data_path is not None + + + + +def test_import_STRING(generate_STRING): + """ + Args: + generate_STRING: + """ + assert generate_STRING.data_path is not None + + +def test_annotate_STRING(generate_TCGA_LUAD, generate_STRING): + """ + Args: + generate_TCGA_LUAD: + generate_STRING: + """ + generate_TCGA_LUAD.Protein.annotate_sequences(generate_STRING, on="protein_name") + assert not generate_TCGA_LUAD.Protein.annotations["sequence"].empty + + +# def test_get_interactions_lnc2target(generate_LncRNA2Target): +# assert generate_LncRNA2Target.get_interactions() is not None