def to_association(gaf_line: List[str], report=None, group="unknown", dataset="unknown", qualifier_parser=assocparser.Qualifier2_1(), bio_entities=None) -> assocparser.ParseResult:
report = Report(group=group, dataset=dataset) if report is None else report
bio_entities = collections.BioEntities(dict()) if bio_entities is None else bio_entities
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[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)
parsed_taxons_result = gaf_line_validators["taxon"].validate(gaf_line[TAXON_INDEX]) # type: assocparser.ValidateResult
if not parsed_taxons_result.valid:
report.error(source_line, Report.INVALID_TAXON, parsed_taxons_result.original, parsed_taxons_result.message, taxon=parsed_taxons_result.original, rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
taxon = parsed_taxons_result.parsed[0]
date = assocparser.parse_date(gaf_line[13], report, source_line)
if date is None:
return assocparser.ParseResult(source_line, [], True, report=report)
interacting_taxon = parsed_taxons_result.parsed[1] if len(parsed_taxons_result.parsed) == 2 else None
subject_curie = association.Curie(gaf_line[0], gaf_line[1])
subject = association.Subject(subject_curie, gaf_line[2], [gaf_line[9]], gaf_line[10].split("|"), [association.map_gp_type_label_to_curie(gaf_line[11])], taxon)
gpi_entity = bio_entities.get(subject_curie)
if gpi_entity is not None and subject != gpi_entity:
subject = gpi_entity
# column 4 is qualifiers -> index 3
# For allowed, see http://geneontology.org/docs/go-annotations/#annotation-qualifiers
# We use the below validate to check validaty if qualifiers, not as much to *parse* them into the GoAssociation object.
# For GoAssociation we will use the above qualifiers list. This is fine because the above does not include `NOT`, etc
# This is confusing, and we can fix later on by consolidating qualifier and relation in GoAssociation.
parsed_qualifiers = qualifier_parser.validate(gaf_line[3])
if not parsed_qualifiers.valid:
report.error(source_line, Report.INVALID_QUALIFIER, parsed_qualifiers.original, parsed_qualifiers.message, taxon=gaf_line[TAXON_INDEX], rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
aspect = gaf_line[8]
negated, relation_label, qualifiers = assocparser._parse_qualifier(gaf_line[3], aspect)
# Note: Relation label is grabbed from qualifiers, if any exist in _parse_qualifier
qualifiers = [association.Curie.from_str(curie_util.contract_uri(relations.lookup_label(q), strict=False)[0]) for q in qualifiers]
object = association.Term(association.Curie.from_str(gaf_line[4]), taxon)
if isinstance(object, association.Error):
report.error(source_line, Report.INVALID_SYMBOL, gaf_line[4], "Problem parsing GO Term", taxon=gaf_line[TAXON_INDEX], rule=1)
# References
references = [association.Curie.from_str(e) for e in gaf_line[5].split("|") if e]
for r in references:
if isinstance(r, association.Error):
report.error(source_line, Report.INVALID_SYMBOL, gaf_line[5], "Problem parsing references", taxon=gaf_line[TAXON_INDEX], rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
gorefs = [ref for ref in references if ref.namespace == "GO_REF"] + [None]
eco_curie = ecomap.coderef_to_ecoclass(gaf_line[6], reference=gorefs[0])
if eco_curie is None:
report.error(source_line, Report.UNKNOWN_EVIDENCE_CLASS, gaf_line[6], msg="Expecting a known ECO GAF code, e.g ISS", rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
withfroms = association.ConjunctiveSet.str_to_conjunctions(gaf_line[7])
if isinstance(withfroms, association.Error):
report.error(source_line, Report.INVALID_SYMBOL, gaf_line[7], "Problem parsing with/from", taxon=gaf_line[TAXON_INDEX], rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
evidence_type = association.Curie.from_str(eco_curie)
if isinstance(evidence_type, association.Error):
report.error(source_line, Report.INVALID_SYMBOL, gaf_line[6], "Problem parsing evidence type", taxon=gaf_line[TAXON_INDEX], rule=1)
evidence = association.Evidence(association.Curie.from_str(eco_curie), references, withfroms)
if any([isinstance(e, association.Error) for e in evidence.has_supporting_reference]):
first_error = [e for e in evidence.has_supporting_reference if isinstance(e, association.Error)][0]
report.error(source_line, Report.INVALID_SYMBOL, gaf_line[5], first_error.info, taxon=str(taxon), rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
subject_extensions = []
if gaf_line[16]:
subject_filler = association.Curie.from_str(gaf_line[16])
if isinstance(subject_filler, association.Error):
report.error(source_line, assocparser.Report.INVALID_ID, gaf_line[16], subject_filler.info, taxon=str(taxon), rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
# filler is not an Error, so keep moving
subject_extensions.append(association.ExtensionUnit(association.Curie.from_str("rdfs:subClassOf"), subject_filler))
conjunctions = []
if gaf_line[15]:
conjunctions = association.ConjunctiveSet.str_to_conjunctions(
gaf_line[15],
conjunct_element_builder=lambda el: association.ExtensionUnit.from_str(el))
if isinstance(conjunctions, association.Error):
report.error(source_line, Report.EXTENSION_SYNTAX_ERROR, conjunctions.info, "extensions should be relation(curie) and relation should have corresponding URI", taxon=str(taxon), rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
relation_uri = relations.lookup_label(relation_label)
if relation_uri is None:
report.error(source_line, assocparser.Report.INVALID_QUALIFIER, relation_label, "Could not find CURIE for relation `{}`".format(relation_label), taxon=str(taxon), rule=1)
return assocparser.ParseResult(source_line, [], True, report=report)
# We don't have to check that this is well formed because we're grabbing it from the known relations URI map.
relation_curie = association.Curie.from_str(curie_util.contract_uri(relation_uri)[0])
a = association.GoAssociation(
source_line="\t".join(gaf_line),
subject=subject,
relation=relation_curie,
object=object,
negated=negated,
qualifiers=qualifiers,
aspect=aspect,
interacting_taxon=interacting_taxon,
evidence=evidence,
subject_extensions=subject_extensions,
object_extensions=conjunctions,
provided_by=gaf_line[14],
date=date,
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)
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(
gaf_line: List[str],
report=None,
group="unknown",
dataset="unknown",
qualifier_parser=Qualifier2_1()) -> 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")
date = assocparser._normalize_gaf_date(gaf_line[13], report, taxon_curie,
source_line)
if date is None:
return assocparser.ParseResult(source_line, [], True, report=report)
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)
# column 4 is qualifiers -> index 3
# For allowed, see http://geneontology.org/docs/go-annotations/#annotation-qualifiers
parsed_qualifiers = qualifier_parser.validate(gaf_line[3])
if not parsed_qualifiers.valid:
report.error(source_line,
Report.INVALID_QUALIFIER,
parsed_qualifiers.original,
parsed_qualifiers.message,
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],
association.ConjunctiveSet.str_to_conjunctions(gaf_line[7]))
subject_extensions = [
association.ExtensionUnit("rdfs:subClassOf", gaf_line[16])
] if gaf_line[16] else []
conjunctions = []
if gaf_line[15]:
conjunctions = association.ConjunctiveSet.str_to_conjunctions(
gaf_line[15],
conjunct_element_builder=lambda el: association.ExtensionUnit.
from_str(el))
if isinstance(conjunctions, association.Error):
report.error(source_line,
Report.EXTENSION_SYNTAX_ERROR,
conjunctions.info,
"extensions should be relation(curie)",
taxon=taxon,
rule=1)
return assocparser.ParseResult(source_line, [],
True,
report=report)
looked_up_rel = relations.lookup_label(relation)
if looked_up_rel is None:
report.error(source_line,
assocparser.Report.INVALID_QUALIFIER,
relation,
"Could not find CURIE for relation `{}`".format(relation),
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=conjunctions,
provided_by=gaf_line[14],
date=date,
properties={})
return assocparser.ParseResult(source_line, [a], False, report=report)