def _test_path_bp_mf(branch_dist, godag, prt):
"""Test distances between BP branch and MF branch."""
go_mf = 'GO:0003676' # level-03 depth-03 nucleic acid binding [molecular_function]
go_bp = 'GO:0007516' # level-04 depth-05 hemocyte development [biological_process]
dst_none = semantic_distance(go_mf, go_bp, godag)
sim_none = semantic_similarity(go_mf, go_bp, godag)
assc = dnld_assc("gene_association.tair", godag)
termcounts = TermCounts(godag, assc)
fmt = '({GO1}, {GO2}) {TYPE:6} score = {VAL}\n'
sim_r = resnik_sim(go_mf, go_bp, godag, termcounts)
sim_l = lin_sim(go_mf, go_bp, godag, termcounts)
if prt is not None:
prt.write(
fmt.format(TYPE='semantic distance',
GO1=go_mf,
GO2=go_bp,
VAL=dst_none))
prt.write(
fmt.format(TYPE='semantic similarity',
GO1=go_mf,
GO2=go_bp,
VAL=sim_none))
prt.write(
fmt.format(TYPE='Resnik similarity',
GO1=go_mf,
GO2=go_bp,
VAL=sim_r))
prt.write(
fmt.format(TYPE='Lin similarity', GO1=go_mf, GO2=go_bp, VAL=sim_l))
assert dst_none is None
assert sim_none is None
assert sim_r is None
assert sim_l is None
sim_d = semantic_distance(go_mf, go_bp, godag, branch_dist)
if prt is not None:
prt.write(
fmt.format(TYPE='semantic distance',
GO1=go_mf,
GO2=go_bp,
VAL=sim_d))
assert sim_d == godag[go_mf].depth + godag[go_bp].depth + branch_dist
def _test_path_same(godag, prt):
"""Test distances btween GO IDs on the same path."""
goid_bottom = 'GO:0007516' # level-04 depth-05 hemocyte development [biological_process]
# Test distances up the same branch
goids_bp = [
'GO:0008150', # level-00 depth-00 biological_process [biological_process]
'GO:0009987', # level-01 depth-01 cellular process [biological_process]
'GO:0044763', # level-02 depth-02 single-organism cellular process [biological_process]
'GO:0048869', # level-03 depth-03 cellular developmental process [biological_process]
'GO:0048468'] # level-03 depth-04 cell development [biological_process]
fmt = '{DST} semantic_distance for {GO1} and {GO2} on the same branch\n'
for dst_exp, goid in enumerate(reversed(goids_bp), 1):
dst_act = semantic_distance(goid_bottom, goid, godag)
if prt is not None:
prt.write(fmt.format(DST=dst_act, GO1=goid_bottom, GO2=goid))
assert dst_act == dst_exp
def _test_path_parallel(godag, prt):
"""Test distances between GO IDs on parallel branches."""
goid_bottom = 'GO:0007516' # BP level-04 depth-05 hemocyte development
# Test distances up a parallel branch
goids = [
'GO:0044763', # BP level-02 depth-02 single-organism cellular process
'GO:0008219', # BP level-03 depth-03 cell death
'GO:0070997', # BP level-04 depth-04 neuron death
'GO:0036475', # BP level-05 depth-05 neuron death in response to oxidative stress
'GO:0036476'] # BP level-06 depth-06 neuron death in response to hydrogen peroxide
fmt = '{DST} semantic_distance between {GO1} and {GO2} on parallel branches\n'
for dst_exp, goid in enumerate(goids, 3):
dst_act = semantic_distance(goid_bottom, goid, godag)
if prt is not None:
prt.write(fmt.format(DST=dst_act, GO1=goid_bottom, GO2=goid))
assert dst_act == dst_exp