def make_conjunctions(extension: List) -> association.ExtensionConjunctions:
extension_units = [] # type: List[association.ExtensionUnit]
for unit in extension:
extension_units.append(
association.ExtensionUnit(unit["relation"], unit["term"]))
return association.ExtensionConjunctions(frozenset(extension_units))
def make_keys_from_gaf(gaf: List[str]) -> List[AnnotationKey]:
term = curie_util.expand_uri(gaf[4], cmaps=[prefix_context])
relation = aspect_relation_map[gaf[8]]
taxon = "http://purl.obolibrary.org/obo/NCBITaxon_{}".format(
gaf[12].split("|")[0].split(":")[1])
extension = gaf[15]
annotation_keys = [] # type: List[AnnotationKey]
for conjunction in extension.split("|"):
# conjunction is foo(bar),hello(world)
conjunctions = [] # type: List[association.ExtensionUnit]
for extension_unit in conjunction.split(","):
# extension_unit is foo(bar)
found_rel = relation_tuple.match(extension_unit)
if found_rel:
rel_label, filler = found_rel.groups()
ext_relation = lookup_relation(rel_label) # type: Uri
fill_id = curie_util.expand_uri(filler, cmaps=[prefix_context
]) # type: Uri
extension_unit = association.ExtensionUnit(
ext_relation, fill_id) # type: association.ExtensionUnit
# Append the extensions unit to the list of conjunctions
conjunctions.append(extension_unit)
extension_conjunction = association.ExtensionConjunctions(
frozenset(conjunctions))
# Build the Key now
annotation_keys.append(
AnnotationKey(RelationTo(relation, term), taxon,
extension_conjunction))
return annotation_keys
def test_build_annotation_inferences():
with open("tests/resources/test.inferences.json") as inferences_file:
gaferences = json.load(inferences_file)
inferences = gaference.build_annotation_inferences(gaferences)
akey = gaference.AnnotationKey(
gaference.RelationTo("http://purl.obolibrary.org/obo/BFO_0000050",
"http://purl.obolibrary.org/obo/GO_0036064"),
"http://purl.obolibrary.org/obo/NCBITaxon_10090",
association.ExtensionConjunctions(
frozenset([
association.ExtensionUnit(
"http://purl.obolibrary.org/obo/BFO_0000050",
"http://purl.obolibrary.org/obo/EMAPA_17168"),
association.ExtensionUnit(
"http://purl.obolibrary.org/obo/BFO_0000050",
"http://purl.obolibrary.org/obo/CL_0010009")
])))
val = inferences[akey]
expected = gaference.InferenceValue(True, False, [
gaference.RelationTo("http://purl.obolibrary.org/obo/BFO_0000050",
"http://purl.obolibrary.org/obo/GO_0097458")
])
assert val == expected
def make_keys_from_gaf(gaf: association.GoAssociation) -> List[AnnotationKey]:
term = curie_util.expand_uri(gaf.object.id, cmaps=[prefix_context])
relation = curie_util.expand_uri(gaf.relation, cmaps=[prefix_context])
taxon = curie_util.expand_uri(gaf.object.taxon, cmaps=[prefix_context])
extensions = gaf.object_extensions
annotation_keys = [] # type: List[AnnotationKey]
if extensions.conjunctions:
for conjunction in extensions.conjunctions:
# conjunction is foo(bar),hello(world)
extension_conjunction = association.ExtensionConjunctions(
frozenset(conjunction.extensions))
# Build the Key now
annotation_keys.append(
AnnotationKey(RelationTo(relation, term), taxon,
extension_conjunction))
else:
annotation_keys.append(
AnnotationKey(RelationTo(relation, term), taxon,
association.ExtensionConjunctions(frozenset([]))))
return annotation_keys
def to_association(gaf_line: List[str],
report=None,
group="unknown",
dataset="unknown") -> assocparser.ParseResult:
report = Report(group=group, dataset=dataset) if report is None else report
source_line = "\t".join(gaf_line)
if source_line == "":
report.error(source_line,
"Blank Line",
"EMPTY",
"Blank lines are not allowed",
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
if len(gaf_line) > 17:
# If we see more than 17 columns, we will just cut off the columns after column 17
report.warning(
source_line,
assocparser.Report.WRONG_NUMBER_OF_COLUMNS,
"",
msg=
"There were more than 17 columns in this line. Proceeding by cutting off extra columns after column 17.",
rule=1)
gaf_line = gaf_line[:17]
if 17 > len(gaf_line) >= 15:
gaf_line += [""] * (17 - len(gaf_line))
if len(gaf_line) != 17:
report.error(
source_line,
assocparser.Report.WRONG_NUMBER_OF_COLUMNS,
"",
msg=
"There were {columns} columns found in this line, and there should be 15 (for GAF v1) or 17 (for GAF v2)"
.format(columns=len(gaf_line)),
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
## check for missing columns
## We use indeces here because we run GO RULES before we split the vals into individual variables
DB_INDEX = 0
DB_OBJECT_INDEX = 1
TAXON_INDEX = 12
REFERENCE_INDEX = 5
if gaf_line[DB_INDEX] == "":
report.error(source_line,
Report.INVALID_IDSPACE,
"EMPTY",
"col1 is empty",
taxon=gaf_line[TAXON_INDEX],
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
if gaf_line[DB_OBJECT_INDEX] == "":
report.error(source_line,
Report.INVALID_ID,
"EMPTY",
"col2 is empty",
taxon=gaf_line[TAXON_INDEX],
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
if gaf_line[TAXON_INDEX] == "":
report.error(source_line,
Report.INVALID_TAXON,
"EMPTY",
"taxon column is empty",
taxon=gaf_line[TAXON_INDEX],
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
if gaf_line[REFERENCE_INDEX] == "":
report.error(source_line,
Report.INVALID_ID,
"EMPTY",
"reference column 6 is empty",
taxon=gaf_line[TAXON_INDEX],
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
taxon = gaf_line[12].split("|")
taxon_curie = taxon[0].replace("taxon", "NCBITaxon")
interacting_taxon = taxon[1].replace(
"taxon", "NCBITaxon") if len(taxon) == 2 else None
subject_curie = "{db}:{id}".format(db=gaf_line[0], id=gaf_line[1])
subject = association.Subject(subject_curie, gaf_line[2], gaf_line[9],
gaf_line[10].split("|"), gaf_line[11],
taxon_curie)
aspect = gaf_line[8]
negated, relation, qualifiers = assocparser._parse_qualifier(
gaf_line[3], aspect)
# For allowed, see http://geneontology.org/docs/go-annotations/#annotation-qualifiers
for q in qualifiers:
if q not in allowed_qualifiers:
report.error(
source_line,
Report.INVALID_QUALIFIER,
q,
"Qualifiers must be `contributes_to`, `colocalizes_with`, or `NOT`",
taxon=gaf_line[TAXON_INDEX],
rule=1)
return assocparser.ParseResult(source_line, [],
True,
report=report)
object = association.Term(gaf_line[4], taxon_curie)
evidence = association.Evidence(ecomap.coderef_to_ecoclass(gaf_line[6]),
[e for e in gaf_line[5].split("|") if e],
[e for e in gaf_line[7].split("|") if e])
subject_extensions = [
association.ExtensionUnit("rdfs:subClassOf", gaf_line[16])
] if gaf_line[16] else []
conjunctions = []
if gaf_line[15]:
for conjuncts in gaf_line[15].split("|"):
extension_units = []
for u in conjuncts.split(","):
parsed = relation_tuple.findall(u)
if len(parsed) == 1:
rel, term = parsed[0]
extension_units.append(association.ExtensionUnit(
rel, term))
else:
# Otherwise, something went bad with the regex, and it's a bad parse
report.error(source_line,
Report.EXTENSION_SYNTAX_ERROR,
u,
"extensions should be relation(curie)",
taxon=taxon,
rule=1)
return assocparser.ParseResult(source_line, [],
True,
report=report)
conjunction = association.ExtensionConjunctions(extension_units)
conjunctions.append(conjunction)
object_extensions = association.ExtensionExpression(conjunctions)
looked_up_rel = relations.lookup_label(relation)
if looked_up_rel is None:
report.error(
source_line,
assocparser.Report.INVALID_QUALIFIER,
relation,
"Qualifer must be \"colocalizes_with\", \"contributes_to\", or \"NOT\"",
taxon=taxon,
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
a = association.GoAssociation(
source_line="\t".join(gaf_line),
subject=subject,
relation=curie_util.contract_uri(looked_up_rel)[0],
object=object,
negated=negated,
qualifiers=qualifiers,
aspect=aspect,
interacting_taxon=interacting_taxon,
evidence=evidence,
subject_extensions=subject_extensions,
object_extensions=object_extensions,
provided_by=gaf_line[14],
date=gaf_line[13],
properties={})
return assocparser.ParseResult(source_line, [a], False, report=report)
def to_association(gpad_line: List[str],
report=None,
group="unknown",
dataset="unknown") -> assocparser.ParseResult:
report = Report(group=group, dataset=dataset) if report is None else report
source_line = "\t".join(gpad_line)
if len(gpad_line) > 12:
report.warning(
source_line,
assocparser.Report.WRONG_NUMBER_OF_COLUMNS,
"",
msg=
"There were more than 12 columns in this line. Proceeding by cutting off extra columns.",
rule=1)
gpad_line = gpad_line[:12]
if 12 > len(gpad_line) >= 10:
gpad_line += [""] * (12 - len(gpad_line))
if len(gpad_line) != 12:
report.error(
source_line,
assocparser.Report.WRONG_NUMBER_OF_COLUMNS,
"",
msg=
"There were {columns} columns found in this line, and there should be between 10 and 12"
.format(columns=len(gpad_line)))
return assocparser.ParseResult(source_line, [], True, report=report)
## check for missing columns
## We use indeces here because we run GO RULES before we split the vals into individual variables
DB_INDEX = 0
DB_OBJECT_INDEX = 1
QUALIFIER = 2
REFERENCE_INDEX = 4
EVIDENCE_INDEX = 5
if gpad_line[DB_INDEX] == "":
report.error(source_line,
Report.INVALID_IDSPACE,
"EMPTY",
"col1 is empty",
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
if gpad_line[DB_OBJECT_INDEX] == "":
report.error(source_line,
Report.INVALID_ID,
"EMPTY",
"col2 is empty",
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
if gpad_line[QUALIFIER] == "":
report.error(source_line,
Report.INVALID_TAXON,
"EMPTY",
"qualifier column is empty",
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
if gpad_line[REFERENCE_INDEX] == "":
report.error(source_line,
Report.INVALID_ID,
"EMPTY",
"reference column is empty",
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
if gpad_line[EVIDENCE_INDEX] == "":
report.error(source_line,
Report.INVALID_ID,
"EMPTY",
"Evidence column is empty",
rule=1)
taxon = ""
subject_curie = "{db}:{id}".format(db=gpad_line[0], id=gpad_line[1])
subject = association.Subject(subject_curie, "", "", [], "", "")
object = association.Term(gpad_line[3], "")
evidence = association.Evidence(gpad_line[5],
[e for e in gpad_line[4].split("|") if e],
[e for e in gpad_line[6].split("|") if e])
raw_qs = gpad_line[2].split("|")
negated = "NOT" in raw_qs
looked_up_qualifiers = [
relations.lookup_label(q) for q in raw_qs if q != "NOT"
]
if None in looked_up_qualifiers:
report.error(source_line,
Report.INVALID_QUALIFIER,
raw_qs,
"Could not find a URI for qualifier",
taxon=taxon,
rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
qualifiers = [curie_util.contract_uri(q)[0] for q in looked_up_qualifiers]
conjunctions = []
if gpad_line[11]:
for conjuncts in gpad_line[11].split("|"):
extension_units = []
for u in conjuncts.split(","):
parsed = relation_tuple.findall(u)
if len(parsed) == 1:
rel, term = parsed[0]
extension_units.append(association.ExtensionUnit(
rel, term))
else:
# Otherwise, something went bad with the regex, and it's a bad parse
report.error(source_line,
Report.EXTENSION_SYNTAX_ERROR,
u,
"extensions should be relation(curie)",
taxon=taxon,
rule=1)
return assocparser.ParseResult(source_line, [],
True,
report=report)
conjunction = association.ExtensionConjunctions(extension_units)
conjunctions.append(conjunction)
object_extensions = association.ExtensionExpression(conjunctions)
properties_list = [
prop.split("=") for prop in gpad_line[11].split("|") if prop
]
# print(properties_list)
a = association.GoAssociation(
source_line="\t".join(gpad_line),
subject=subject,
relation="",
object=object,
negated=negated,
qualifiers=qualifiers,
aspect=None,
interacting_taxon=gpad_line[7],
evidence=evidence,
subject_extensions=[],
object_extensions=object_extensions,
provided_by=gpad_line[9],
date=gpad_line[8],
properties={prop[0]: prop[1]
for prop in properties_list if prop})
return assocparser.ParseResult(source_line, [a], False, report=report)