Diff of /tests/test_interaction.py [000000] .. [548210]

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+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