def test_no_optional_attrs():
"""Test loading DAG with no optional attributes."""
obj = OptionalAttrs("go-basic.obo", None)
obj.chk_no_optattrs()
obj = OptionalAttrs("go-basic.obo", [])
obj.chk_no_optattrs()
obj = OptionalAttrs("go-basic.obo", set([]))
obj.chk_no_optattrs()
def test_optional_attrs():
"""Test loading optional GO term field, 'synonym'."""
# Summary for all fields in a GO DAG
opt_attrs = ['relationship']
obj = OptionalAttrs("go-basic.obo", opt_attrs)
# RELATIONSHIP: Stored in a dict with values being sets of GO IDs
for rel in [
'part_of', 'regulates', 'negatively_regulates',
'positively_regulates'
]:
obj.chk_relationships_rev(rel, prt=None)
print("PASSED: relationship: {REL}".format(REL=rel))
obj.prt_summary()
obj.chk_get_goterms_upper()
obj.chk_get_goterms_lower()
def test_optional_attrs():
"""Test loading optional GO term field, 'synonym'."""
# Summary for all fields in a GO DAG
opt_attrs = ['relationship']
obj = OptionalAttrs("go-basic.obo", opt_attrs)
# RELATIONSHIP: Stored in a dict with values being sets of GO IDs
for rel in ['part_of', 'regulates', 'negatively_regulates', 'positively_regulates']:
obj.chk_relationships_rev(rel, prt=None)
print("PASSED: relationship: {REL}".format(REL=rel))
obj.prt_summary()
obj.chk_get_goterms_upper()
obj.chk_get_goterms_lower()
def test_no_optional_attrs():
"""Test loading DAG with no optional attributes."""
obj = OptionalAttrs("go-basic.obo", None)
obj.chk_no_optattrs()
def test_optional_attrs():
"""Test loading optional GO term field, 'synonym'."""
prt = sys.stdout
prt = None
# Summary for all fields in a GO DAG
opt_attrs = ['def', 'comment', 'subset', 'synonym', 'xref', 'relationship']
obj = OptionalAttrs("go-basic.obo", opt_attrs)
obj.prt_summary()
# SCALAR: Check optional attributes whose information is stored in string
for attr in ['defn', 'comment']:
# Check that all GOTerms have a string; ACTUAL matches EXPECTED if present, else ""
obj.chk_str(attr)
print("PASSED COUNT TEST: {ATTR}".format(ATTR=attr))
# SET: Check optional attributes whose information is stored in a set
# Check that all GO IDs that should have relationships do have relationships.
# For each GO ID, check that actual count of a set attr equals expected count
obj.chk_set('subset')
print("PASSED: subset")
# RELATIONSHIP: Stored in a dict with values being sets of GO IDs
obj.chk_relationships()
print("PASSED: relationship")
# SYNONYM: Synonyms are stored in a list of namedtuples
obj.chk_synonyms(prt)
print("PASSED: synonyms")
# XREF: Stored in a set
obj.chk_xref(prt)
print("PASSED: xrefs")
def test_optional_attrs():
"""Test loading optional GO term field, 'synonym'."""
args = set(sys.argv[1:])
prt = sys.stdout if 'prt' in args else None
exit_if_warning = 'die' in args
# Summary for all fields in a GO DAG
opt_attrs = ['def', 'comment', 'subset', 'synonym', 'xref', 'relationship']
obj = OptionalAttrs("go-basic.obo", opt_attrs)
obj.prt_summary()
# SCALAR: Check optional attributes whose information is stored in string
for attr in ['defn', 'comment']:
# Check that all GOTerms have a string; ACTUAL matches EXPECTED if present, else ""
obj.chk_str(attr)
print("PASSED COUNT TEST: {ATTR}".format(ATTR=attr))
# SET: Check optional attributes whose information is stored in a set
# Check that all GO IDs that should have relationships do have relationships.
# For each GO ID, check that actual count of a set attr equals expected count
obj.chk_set('subset')
print("PASSED: subset")
# RELATIONSHIP: Stored in a dict with values being sets of GO IDs
obj.chk_relationships()
print("PASSED: relationship")
# SYNONYM: Synonyms are stored in a list of namedtuples
badnts = obj.chk_synonyms(prt)
_prt_badnts(badnts, exit_if_warning)
print("PASSED: synonyms")
# XREF: Stored in a set
obj.chk_xref(prt)
print("PASSED: xrefs")