How to use bioservices - 10 common examples

def test_muscle():
    m = MUSCLE(verbose=False)
    m.parameters
    m.getParametersDetails("format")

    u = uniprot.UniProt(verbose=False)
    f1 = u.get_fasta("P18812")
    f2 = u.get_fasta("P18813")

    jobid = m.run(frmt="fasta", sequence=f1+f2, email="cokelaer@ebi.ac.uk")
    m.getStatus(jobid)
    m.wait(jobid)

    m.getResultTypes(jobid)
    m.getResult(jobid, 'phylotree')

def test_chebi():
    ch = ChEBI()
    ch.getCompleteEntity("CHEBI:10102")
    res = ch.conv("CHEBI:10102", "KEGG COMPOUND accession")
    assert res == ['C07484']

    try:
        res = ch.conv("CHEBI:10102", "wrong db")
        assert False
    except:
        assert True

    ch.getOntologyChildren("CHEBI:27732")
    ch.getOntologyParents("CHEBI:27732")
    ch.getUpdatedPolymer("CHEBI:27732")

def test_chebi_mass():
    ch = ChEBI()
    mass1 = ch.getCompleteEntity("CHEBI:27732").mass
    assert float(mass1) == 194.19076

def biomodels():
    return BioModels(verbose=False)

def uniprot():
    u = UniProt(verbose=False, cache=False)
    u.logging.level = "ERROR"
    return u

def test_get():
    pc2 = pathwaycommons.PathwayCommons(verbose=False)
    pc2.get("col5a1")
    pc2.get("http://identifiers.org/uniprot/Q06609")

def test_idmapping():
    pc2 = pathwaycommons.PathwayCommons(verbose=False)
    pc2.idmapping("BRCA2")
    pc2.idmapping(["TP53", "BRCA2"])

def test_graph(): 
    pc2 = pathwaycommons.PathwayCommons(verbose=False)
    res = pc2.graph(source="http://identifiers.org/uniprot/P20908",
            kind="neighborhood", frmt="EXTENDED_BINARY_SIF")

def test_top_pathways():
    pc2 = pathwaycommons.PathwayCommons(verbose=False)
    res = pc2.top_pathways()

def test_traverse():
     pc2 = pathwaycommons.PathwayCommons(verbose=False)
     res = pc2.traverse(
        uri=['http://identifiers.org/uniprot/P38398', 'http://identifiers.org/uniprot/Q06609'], 
        path="ProteinReference/organism")
     #res = pc2.traverse(