def to_gaf_2_2_tsv(self) -> List:
gp_isoforms = "" if not self.subject_extensions else self.subject_extensions[
0].term
qual_labels = [
relations.lookup_uri(curie_util.expand_uri(str(q), strict=False))
for q in self.qualifiers
]
if self.negated:
qual_labels.insert(0, "NOT")
qualifier = "|".join(qual_labels)
self.object.taxon.namespace = "taxon"
taxon = str(self.object.taxon)
if self.interacting_taxon:
self.interacting_taxon.namespace = "taxon"
taxon = "{taxon}|{interacting}".format(taxon=taxon,
interacting=str(
self.interacting_taxon))
return [
self.subject.id.namespace, self.subject.id.identity,
self.subject.label, qualifier,
str(self.object.id), "|".join(
[str(ref) for ref in self.evidence.has_supporting_reference]),
ecomap.ecoclass_to_coderef(str(self.evidence.type))[0],
ConjunctiveSet.list_to_str(self.evidence.with_support_from),
self.aspect if self.aspect else "", self.subject.fullname,
"|".join(self.subject.synonyms), self.subject.type, taxon,
self.date, self.provided_by,
ConjunctiveSet.list_to_str(self.object_extensions), gp_isoforms
]
def to_gaf_2_1_tsv(self) -> List:
"""
Converts the GoAssociation into a "TSV" columnar GAF 2.1 row as a list of strings.
"""
gp_isoforms = "" if not self.subject_extensions else self.subject_extensions[
0].term
allowed_qualifiers = {"contributes_to", "colocalizes_with"}
# Curie Object -> CURIE Str -> URI -> Label
qual_labels = [
relations.lookup_uri(curie_util.expand_uri(str(q), strict=False))
for q in self.qualifiers
]
if len(qual_labels) == 1 and qual_labels[0] not in allowed_qualifiers:
logger.warning(
"Cannot write qualifier `{}` in GAF version 2.1 since only {} are allowed: skipping"
.format(self.qualifiers[0], ", ".join(allowed_qualifiers)))
# If the qualifier is wrong, blank out the qualifiers
qual_labels = []
if self.negated:
qual_labels.append("NOT")
qualifier = "|".join(qual_labels)
self.object.taxon.namespace = "taxon"
taxon = str(self.object.taxon)
if self.interacting_taxon:
self.interacting_taxon.namespace = "taxon"
taxon = "{taxon}|{interacting}".format(taxon=taxon,
interacting=str(
self.interacting_taxon))
# For extensions, we provide the to string function on ConjunctElement that
# calls its `display` method, with the flag to use labels instead of the CURIE.
# This function is used to turn the whole column correctly into a string
return [
self.subject.id.namespace, self.subject.id.identity,
self.subject.label, qualifier,
str(self.object.id), "|".join(
[str(ref) for ref in self.evidence.has_supporting_reference]),
self.evidence.gaf_evidence_code(),
ConjunctiveSet.list_to_str(self.evidence.with_support_from),
self.aspect if self.aspect else "",
self.subject.fullname_field(), "|".join(self.subject.synonyms),
gp_type_label_to_curie(self.subject.type[0]), taxon,
ymd_str(self.date, ""), self.provided_by,
ConjunctiveSet.list_to_str(
self.object_extensions,
conjunct_to_str=lambda conj: conj.display(use_rel_label=True)),
gp_isoforms
]
def to_gpad_1_2_tsv(self) -> List:
"""
Converts the GoAssociation into a "TSV" columnar GPAD 1.2 row as a list of strings.
"""
# Curie Object -> CURIE Str -> URI -> Label
qual_labels = [
relations.lookup_uri(curie_util.expand_uri(str(q), strict=False))
for q in self.qualifiers
]
# Try qualifiers first since, if we are going from GAF -> GPAD and the GAF had a qualifier, that would be
# more specific than the relation, which is calculated from the aspect/Go term.
if qual_labels == []:
# If there were no qualifiers, then we'll use the Relation. Gpad requires at least one qualifier (which is the relation)
qual_labels.append(
relations.lookup_uri(
curie_util.expand_uri(str(self.relation), strict=False)))
if self.negated:
qual_labels = ["NOT"] + qual_labels
qualifier = "|".join(qual_labels)
props_list = [
"{key}={value}".format(key=key, value=value)
for key, value in self.properties
]
return [
self.subject.id.namespace, self.subject.id.identity, qualifier,
str(self.object.id), "|".join(
[str(ref) for ref in self.evidence.has_supporting_reference]),
str(self.evidence.type),
ConjunctiveSet.list_to_str(self.evidence.with_support_from),
str(self.interacting_taxon) if self.interacting_taxon else "",
ymd_str(self.date, ""), self.provided_by,
ConjunctiveSet.list_to_str(
self.object_extensions,
conjunct_to_str=lambda conj: conj.display(use_rel_label=True)),
"|".join(props_list)
]
def to_gaf_2_2_tsv(self) -> List:
"""
Converts the GoAssociation into a "TSV" columnar GAF 2.2 row as a list of strings.
"""
gp_isoforms = "" if not self.subject_extensions else self.subject_extensions[
0].term
qual_labels = [
relations.lookup_uri(curie_util.expand_uri(str(q), strict=False))
for q in self.qualifiers
]
if self.negated:
qual_labels.insert(0, "NOT")
qualifier = "|".join(qual_labels)
self.object.taxon.namespace = "taxon"
taxon = str(self.object.taxon)
if self.interacting_taxon:
self.interacting_taxon.namespace = "taxon"
taxon = "{taxon}|{interacting}".format(taxon=taxon,
interacting=str(
self.interacting_taxon))
return [
self.subject.id.namespace, self.subject.id.identity,
self.subject.label, qualifier,
str(self.object.id), "|".join(
[str(ref) for ref in self.evidence.has_supporting_reference]),
self.evidence.gaf_evidence_code(),
ConjunctiveSet.list_to_str(self.evidence.with_support_from),
self.aspect if self.aspect else "",
self.subject.fullname_field(), "|".join(self.subject.synonyms),
gp_type_label_to_curie(self.subject.type[0]), taxon,
ymd_str(self.date, ""), self.provided_by,
ConjunctiveSet.list_to_str(
self.object_extensions,
conjunct_to_str=lambda conj: conj.display(use_rel_label=True)),
gp_isoforms
]
def __relation_to_label(self) -> str:
# Curie -> expand to URI -> reverse relation lookup Label
return relations.lookup_uri(relations.curie_to_obo_uri(self.relation))
def __relation_to_label(self) -> str:
# Curie -> expand to URI -> reverse relation lookup Label
return relations.lookup_uri(
curie_util.expand_uri(str(self.relation), strict=False))