Python Preassembler._generate_relation_tuples Examples

Example #1

File: test_preassembler.py Project: sorgerlab/indra

def test_split_idx():
    ras = Agent('RAS', db_refs={'FPLX': 'RAS'})
    kras = Agent('KRAS', db_refs={'HGNC': '6407'})
    hras = Agent('HRAS', db_refs={'HGNC': '5173'})
    st1 = Phosphorylation(Agent('x'), ras)
    st2 = Phosphorylation(Agent('x'), kras)
    st3 = Phosphorylation(Agent('x'), hras)
    pa = Preassembler(bio_ontology)
    maps = pa._generate_id_maps([st1, st2, st3])
    assert (1, 0) in maps, maps
    assert (2, 0) in maps, maps
    assert pa._comparison_counter == 2
    pa = Preassembler(bio_ontology)
    maps = pa._generate_id_maps([st1, st2, st3], split_idx=1)
    assert (2, 0) in maps, maps
    assert (1, 0) not in maps, maps
    assert pa._comparison_counter == 1

    # Test other endpoints
    refinements = pa._generate_relations([st1, st2, st3])
    assert refinements == \
        {st2.get_hash(): {st1.get_hash()},
         st3.get_hash(): {st1.get_hash()}}, refinements

    refinements = pa._generate_relation_tuples([st1, st2, st3])
    assert refinements == \
        {(st2.get_hash(), st1.get_hash()),
         (st3.get_hash(), st1.get_hash())}