def test_getIsoformFeatures():
c = create_network.CreateNetwork("test", "gencode")
c._txs.add_node("ENST01.2", "1")
c._txs.add_node("ENST02.2", "1")
c._txs.add_node("ENST20.1", "1")
c._txs.add_node("ENST08.1", "1")
c._txs.add_node("ENST18.3", "2")
assert not c._txs.nodes()["ENST20.1"]["Pfam"]
assert not c._txs.nodes()["ENST08.1"]["IDR"]
assert not c._txs.nodes()["ENST18.3"]["Prosite"]
c.getIsoformFeatures(dataPath + "features")
assert c._txs.nodes()["ENST01.2"]["Pfam"]["D1"] == {(1,2), (3,4)}
assert len(c._txs.nodes()["ENST01.2"]["Pfam"]) == 1
assert c._txs.nodes()["ENST02.2"]["Pfam"]["D1"] == {(1,2)}
assert c._txs.nodes()["ENST02.2"]["Pfam"]["D2"] == {(3,4)}
assert c._txs.nodes()["ENST02.2"]["Pfam"]["D4"] == {(5,8)}
assert len(c._txs.nodes()["ENST02.2"]["Pfam"]) == 3
assert c._txs.nodes()["ENST20.1"]["Pfam"]["D2"] == {(3,6)}
assert len(c._txs.nodes()["ENST20.1"]["Pfam"]) == 1
assert c._txs.nodes()["ENST08.1"]["IDR"]["I1"] == {(4,13)}
assert c._txs.nodes()["ENST18.3"]["Prosite"]["P1"] == {(23,123)}
with pytest.raises(SpadaError):
c = create_network.CreateNetwork("test", "gencode")
c.getIsoformFeatures(None)
def test_getDomainInteractions():
c = create_network.CreateNetwork("test", "gencode")
c._genes.add_node(gene_id = "A", gene_symbol = "")
c._genes.add_node(gene_id = "B", gene_symbol = "")
c._genes.add_node(gene_id = "C", gene_symbol = "")
c._genes.add_edge(gene_id1 = "A", gene_id2 = "B")
c._genes.add_edge(gene_id1 = "A", gene_id2 = "C")
c._txs.add_node("A1.1", "A")
c._txs.update_node("A1", "Pfam", (0,0), "D1")
c._txs.update_node("A1", "Pfam", (0,0), "D2")
c._txs.update_node("A1", "Pfam", (0,0), "D6")
c._txs.add_node("A2.1", "A")
c._txs.update_node("A2", "Pfam", (0,0), "D1")
c._txs.update_node("A2", "Pfam", (0,0), "D3")
c._txs.add_node("B1.1", "B")
c._txs.update_node("B1", "Pfam", (0,0), "D4")
c._txs.add_node("C1.1", "C")
c._txs.update_node("C1", "Pfam", (0,0), "D5")
c.getDomainInteractions(dataPath + "ddis")
assert c._txs._net.has_edge("A1.1", "B1.1")
assert c._txs._net["A1.1"]["B1.1"]["ddi"] == {frozenset({"D2","D4"}), frozenset({"D6","D4"})}
assert c._txs._net.has_edge("A2.1", "C1.1")
assert c._txs._net["A2.1"]["C1.1"]["ddi"] == {frozenset({"D3","D5"})}
assert not c._txs._net.has_edge("A1.1", "A2.1")
assert not c._txs._net.has_edge("B1.1", "C1.1")
with pytest.raises(SpadaError):
c = create_network.CreateNetwork("test", "gencode")
c.getDomainInteractions(None)
def test_getIsoformSequences():
c = create_network.CreateNetwork("test", "gencode")
c._txs.add_node("ENST12.3", "1")
c._txs.add_node("ENST08.1", "1")
c._txs.add_node("ENST18.3", "2")
c._txs.add_node("ENST02.2", "2")
c._txs.add_node("ENST16.2", "3")
c._txs.add_node("ENST01.2", "3")
c._txs.add_node("ENST09.1", "3")
c._txs.add_node("ENST13.5", "4")
assert not c._txs.nodes()["ENST12.3"]["proteinSequence"]
assert not c._txs.nodes()["ENST08.1"]["proteinSequence"]
assert not c._txs.nodes()["ENST18.3"]["proteinSequence"]
assert not c._txs.nodes()["ENST02.2"]["proteinSequence"]
assert not c._txs.nodes()["ENST16.2"]["proteinSequence"]
assert not c._txs.nodes()["ENST01.2"]["proteinSequence"]
assert not c._txs.nodes()["ENST09.1"]["proteinSequence"]
assert not c._txs.nodes()["ENST13.5"]["proteinSequence"]
c.getIsoformSequences(dataPath + "fasta")
assert c._txs.nodes()["ENST12.3"]["proteinSequence"] == "ASDFAFAFA"
assert c._txs.nodes()["ENST08.1"]["proteinSequence"] == "ASDASDASDASDA"
assert c._txs.nodes()["ENST18.3"]["proteinSequence"] == "ASFASFASF"
assert c._txs.nodes()["ENST02.2"]["proteinSequence"] == "ASFASFAS"
assert c._txs.nodes()["ENST16.2"]["proteinSequence"] == "ABCDEFGHI"
assert c._txs.nodes()["ENST01.2"]["proteinSequence"] == "ASFSAFASFS"
assert c._txs.nodes()["ENST09.1"]["proteinSequence"] == "ASFASFASF"
assert c._txs.nodes()["ENST13.5"]["proteinSequence"] == "ASFASFASASFASF"
with pytest.raises(SpadaError):
c = create_network.CreateNetwork("test", "gencode")
c.getIsoformSequences(None)
def test_init():
c = create_network.CreateNetwork("test", "gencode")
assert type(c._genes).__name__ == 'GENCODEGeneNetwork'
assert type(c._txs).__name__ == 'GENCODETranscriptNetwork'
c = create_network.CreateNetwork("test", "ucsc")
assert type(c._genes).__name__ == 'UCSCGeneNetwork'
assert type(c._txs).__name__ == 'UCSCTranscriptNetwork'
with pytest.raises(SpadaError):
create_network.CreateNetwork("test", "Unexistant")
def test_addAberrant():
c = create_network.CreateNetwork("test", "gencode")
c.addAberrant(dataPath + 'aberrant')
assert c._txs.nodes()["ABC.1"]["gene_id"] == "ENSG08.4"
assert c._txs.nodes()["DE_FG_HI.2"]["gene_id"] == "ENSG00.5"
assert c._txs.nodes()["JKLM-.3"]["gene_id"] == "ENSG00.5"
def test_createNetworks():
c = create_network.CreateNetwork("test", "gencode")
c.createNetworks(dataPath + "gtf")
assert len(c._genes.nodes()) == 16
assert len(c._txs.nodes()) == 25
assert len(c._txs.nodes()["ENST02.2"]["exons"]) == 6
assert c._txs.nodes()["ENST02.2"]["strand"] == "+"
assert c._txs.nodes()["ENST02.2"]["chr"] == "chr1"
assert c._txs.nodes()["ENST02.2"]["CDS"] == [13000, 13023]
assert len(c._txs.nodes()["ENST19.2"]["exons"]) == 1
assert c._txs.nodes()["ENST19.2"]["strand"] == "-"
assert c._txs.nodes()["ENST19.2"]["chr"] == "chr1"
assert not c._txs.nodes()["ENST19.2"]["CDS"]
assert not c._txs.nodes()["ENST19.2"]["main"]
assert len(c._txs.nodes()["ENST12.3"]["exons"]) == 1
assert c._txs.nodes()["ENST12.3"]["strand"] == "+"
assert c._txs.nodes()["ENST12.3"]["chr"] == "chr1"
assert c._txs.nodes()["ENST12.3"]["CDS"] == [69978, 70004]
assert c._txs.nodes()["ENST12.3"]["main"]
assert len([ x for x,i in c._txs.nodes(data=True) if i['main'] ]) == 3
assert "ENSG999" in c._genes.nodes()
assert "ENSG999" in c._genes.nodes()
assert "ENST99.1" in c._txs.nodes()
assert "ENST99.2" in c._txs.nodes()
assert "ENST99.3" in c._txs.nodes()
# test rejected genes, transcript and CDS
assert "bad_status" not in c._genes.nodes()
assert "bad_accepted_tag" not in c._txs.nodes()
assert "bad_status" not in c._txs.nodes()
assert "rejected_status" not in c._txs.nodes()
assert "test" in c._genes.nodes()
assert "test.1" in c._txs.nodes()
assert c._txs.nodes()["test.1"]["CDS"] == None
assert "ENST99.4" not in c._txs.nodes()
assert "ENST99.5" not in c._txs.nodes()
assert "ENST99.NA" not in c._txs.nodes()
with pytest.raises(SpadaError):
c = create_network.CreateNetwork("test", dataPath + 'annotation.pklz', new = False)
c.createNetworks(dataPath + "gtf")
def test_getInteractions():
c = create_network.CreateNetwork("test", "gencode")
c._genes.add_node(gene_id = "A", gene_symbol = "HSPB8")
c._genes.add_node(gene_id = "B", gene_symbol = "HSPB7")
c._genes.add_node(gene_id = "C", gene_symbol = "RPIA")
c._genes.add_node(gene_id = "D", gene_symbol = "WDYHV1")
c._genes.add_node(gene_id = "E", gene_symbol = "KRT15")
c._genes.add_node(gene_id = "F", gene_symbol = "KRT20")
c._genes.add_node(gene_id = "G", gene_symbol = "TPM1")
c._genes.add_node(gene_id = "H", gene_symbol = "KXD1")
c.getInteractions(dataPath + "ppis")
assert c._genes._net.has_edge("A", "B")
assert c._genes._net.has_edge("C", "D")
assert c._genes._net.has_edge("E", "F")
assert c._genes._net.has_edge("G", "H")
assert len(c._genes._net.edges()) == 4
with pytest.raises(SpadaError):
c = create_network.CreateNetwork("test", "gencode")
c.getInteractions(None)
def test_CreateNetwork():
with pytest.raises(SpadaError):
c = create_network.CreateNetwork("test", "madeup")
def test_init():
c = create_network.CreateNetwork("test", "gencode")
c.run(dataPath + "gtf", dataPath + "fasta", dataPath + "mitab",
dataPath + "ddis", dataPath + "features", dataPath + "aberrant")
# gtf
assert len(c._genes.nodes()) == 16
assert len(c._txs.nodes()) == 28 # 22 txs + 3 aberrant
assert len(c._txs.nodes()["ENST02.2"]["exons"]) == 6
assert c._txs.nodes()["ENST02.2"]["strand"] == "+"
assert c._txs.nodes()["ENST02.2"]["chr"] == "chr1"
assert c._txs.nodes()["ENST02.2"]["CDS"] == [13000, 13023]
assert len(c._txs.nodes()["ENST19.2"]["exons"]) == 1
assert c._txs.nodes()["ENST19.2"]["strand"] == "-"
assert c._txs.nodes()["ENST19.2"]["chr"] == "chr1"
assert not c._txs.nodes()["ENST19.2"]["CDS"]
assert not c._txs.nodes()["ENST19.2"]["main"]
assert len(c._txs.nodes()["ENST12.3"]["exons"]) == 1
assert c._txs.nodes()["ENST12.3"]["strand"] == "+"
assert c._txs.nodes()["ENST12.3"]["chr"] == "chr1"
assert c._txs.nodes()["ENST12.3"]["CDS"] == [69978, 70004]
assert c._txs.nodes()["ENST12.3"]["main"]
assert len([x for x, i in c._txs.nodes(data=True) if i['main']]) == 3
assert "ENSG999" in c._genes.nodes()
assert "ENST99.1" in c._txs.nodes()
assert "ENST99.2" in c._txs.nodes()
assert "ENST99.3" in c._txs.nodes()
# test rejected genes, transcript and CDS
assert "bad_status" not in c._genes.nodes()
assert "bad_accepted_tag" not in c._txs.nodes()
assert "bad_status" not in c._txs.nodes()
assert "rejected_status" not in c._txs.nodes()
assert "test" in c._genes.nodes()
assert "test.1" in c._txs.nodes()
assert c._txs.nodes()["test.1"]["CDS"] == None
assert "ENST99.4" not in c._txs.nodes()
assert "ENST99.5" not in c._txs.nodes()
assert "ENST99.NA" not in c._txs.nodes()
# aberrant
assert c._txs.nodes()["ABC.1"]["gene_id"] == "ENSG08.4"
assert c._txs.nodes()["DE_FG_HI.2"]["gene_id"] == "ENSG00.5"
assert c._txs.nodes()["JKLM-.3"]["gene_id"] == "ENSG00.5"
# interactions
assert c._genes._net.number_of_edges() == 2
assert c._genes._net.has_edge("ENSG00.5", "ENSG00.5")
assert c._genes._net.has_edge("ENSG13.1", "ENSG00.5")
# ddis
assert c._txs._net.number_of_edges() == 4
assert c._txs._net.has_edge("ENST01.2", "ENST01.2")
assert c._txs._net.has_edge("ENST01.2", "ENST02.2")
assert c._txs._net.has_edge("ENST02.2", "ENST02.2")
assert c._txs._net.has_edge("ENST20.1", "ENST02.2")
assert not c._txs._net.has_edge("ENST20.1", "ENST01.2")
assert c._txs._net["ENST01.2"]["ENST01.2"]["ddi"] == {frozenset({"D1"})}
assert c._txs._net["ENST01.2"]["ENST02.2"]["ddi"] == {frozenset({"D1"})}
assert c._txs._net["ENST02.2"]["ENST02.2"]["ddi"] == {
frozenset({"D1"}),
frozenset({"D2"}),
frozenset({'D4', 'D2'})
}
assert c._txs._net["ENST20.1"]["ENST02.2"]["ddi"] == {
frozenset({"D2", "D4"}), frozenset({"D2"})
}
# fasta
assert c._txs.nodes()["ENST12.3"]["proteinSequence"] == "ASDFAFAFA"
assert c._txs.nodes()["ENST08.1"]["proteinSequence"] == "ASDASDASDASDA"
assert c._txs.nodes()["ENST18.3"]["proteinSequence"] == "ASFASFASF"
assert c._txs.nodes()["ENST02.2"]["proteinSequence"] == "ASFASFAS"
assert c._txs.nodes()["ENST16.2"]["proteinSequence"] == "ABCDEFGHI"
assert c._txs.nodes()["ENST01.2"]["proteinSequence"] == "ASFSAFASFS"
assert c._txs.nodes()["ENST09.1"]["proteinSequence"] == "ASFASFASF"
assert c._txs.nodes()["ENST13.5"]["proteinSequence"] == "ASFASFASASFASF"
# features
assert c._txs.nodes()["ENST01.2"]["Pfam"]["D1"] == {(1, 2), (3, 4)}
assert len(c._txs.nodes()["ENST01.2"]["Pfam"]) == 1
assert c._txs.nodes()["ENST02.2"]["Pfam"]["D1"] == {(1, 2)}
assert c._txs.nodes()["ENST02.2"]["Pfam"]["D2"] == {(3, 4)}
assert c._txs.nodes()["ENST02.2"]["Pfam"]["D4"] == {(5, 8)}
assert len(c._txs.nodes()["ENST02.2"]["Pfam"]) == 3
assert c._txs.nodes()["ENST20.1"]["Pfam"]["D2"] == {(3, 6)}
assert len(c._txs.nodes()["ENST20.1"]["Pfam"]) == 1
assert c._txs.nodes()["ENST08.1"]["IDR"]["I1"] == {(4, 13)}
assert c._txs.nodes()["ENST18.3"]["Prosite"]["P1"] == {(23, 123)}
assert os.stat('annotation.pklz').st_size > 0