How to use the bioservices.pathwaycommons.PathwayCommons function in bioservices

To help you get started, we’ve selected a few bioservices examples, based on popular ways it is used in public projects.

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github cokelaer / bioservices / test / test_pathwaycommons.py View on Github external
def test_get():
    pc2 = pathwaycommons.PathwayCommons(verbose=False)
    pc2.get("col5a1")
    pc2.get("http://identifiers.org/uniprot/Q06609")
github cokelaer / bioservices / test / test_pathwaycommons.py View on Github external
def test_idmapping():
    pc2 = pathwaycommons.PathwayCommons(verbose=False)
    pc2.idmapping("BRCA2")
    pc2.idmapping(["TP53", "BRCA2"])
github cokelaer / bioservices / test / test_pathwaycommons.py View on Github external
def test_graph(): 
    pc2 = pathwaycommons.PathwayCommons(verbose=False)
    res = pc2.graph(source="http://identifiers.org/uniprot/P20908",
            kind="neighborhood", frmt="EXTENDED_BINARY_SIF")
github cokelaer / bioservices / test / test_pathwaycommons.py View on Github external
def test_top_pathways():
    pc2 = pathwaycommons.PathwayCommons(verbose=False)
    res = pc2.top_pathways()
github cokelaer / bioservices / test / test_pathwaycommons.py View on Github external
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(
github cokelaer / bioservices / test / test_pathwaycommons.py View on Github external
def test_search_queries():
    pc2 = pathwaycommons.PathwayCommons(verbose=False)
    pc2.search("Q06609")
    pc2.search("brca2", type="proteinreference", organism="homo sapiens",
            datasource="pid")
    pc2.search("name:'col5a1'", type="proteinreference", organism=9606)
    pc2.search("a*", page=3)