def test_all_rules():
# pass
config = assocparser.AssocParserConfig(ontology=ontology)
a = make_annotation("GO:0006397", "ANY")
a = ["blah"] * 16
a[4] = "GO:0006397"
a[6] = "ANY"
a[13] = "20180330"
test_results = qc.test_go_rules(a, config)
assert len(test_results.keys()) == 2
assert test_results["GORULE:0000026"].result_type == qc.ResultType.PASS
assert test_results["GORULE:0000029"].result_type == qc.ResultType.PASS
def test_all_rules():
# pass
config = assocparser.AssocParserConfig(ontology=ontology)
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0006397"
a[6] = "ISS"
a[8] = "P"
a[13] = "20180330"
assoc = gafparser.to_association(a).associations[0]
test_results = qc.test_go_rules(assoc, config).all_results
assert len(test_results.keys()) == 22
assert test_results[
qc.GoRules.GoRule26.value].result_type == qc.ResultType.PASS
assert test_results[
qc.GoRules.GoRule29.value].result_type == qc.ResultType.PASS
def test_all_rules():
# pass
config = all_rules_config(ontology=ontology)
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0006397"
a[5] = "PMID:21873635"
a[6] = "ISS"
a[7] = "PomBase:SPAC25B8.17"
a[8] = "P"
a[12] = "taxon:123"
a[13] = "20180330"
assoc = gafparser.to_association(a).associations[0]
test_results = qc.test_go_rules(assoc, config).all_results
assert len(test_results.keys()) == 24
assert test_results[
qc.GoRules.GoRule26.value].result_type == qc.ResultType.PASS
assert test_results[
qc.GoRules.GoRule29.value].result_type == qc.ResultType.PASS
def parse_line(self, line):
"""
Parses a single line of a GAF
Return a tuple `(processed_line, associations)`. Typically
there will be a single association, but in some cases there
may be none (invalid line) or multiple (disjunctive clause in
annotation extensions)
Note: most applications will only need to call this directly if they require fine-grained control of parsing. For most purposes,
:method:`parse_file` can be used over the whole file
Arguments
---------
line : str
A single tab-seperated line from a GAF file
"""
# Returns assocparser.ParseResult
parsed = super().validate_line(line)
if parsed:
return parsed
if self.is_header(line):
return assocparser.ParseResult(line, [{ "header": True, "line": line.strip() }], True)
vals = [el.strip() for el in line.split("\t")]
# GAF v1 is defined as 15 cols, GAF v2 as 17.
# We treat everything as GAF2 by adding two blank columns.
# TODO: check header metadata to see if columns corresponds to declared dataformat version
if 17 > len(vals) >= 15:
vals += [""] * (17 - len(vals))
if len(vals) > 17:
# If we see more than 17 columns, we will just cut off the columns after column 17
self.report.warning(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)
vals = vals[:17]
if len(vals) != 17:
self.report.error(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(vals)),
rule=1)
return assocparser.ParseResult(line, [], True)
[db,
db_object_id,
db_object_symbol,
qualifier,
goid,
reference,
evidence,
withfrom,
aspect,
db_object_name,
db_object_synonym,
db_object_type,
taxon,
date,
assigned_by,
annotation_xp,
gene_product_isoform] = vals
split_line = assocparser.SplitLine(line=line, values=vals, taxon=taxon)
## check for missing columns
if db == "":
self.report.error(line, Report.INVALID_IDSPACE, "EMPTY", "col1 is empty", taxon=taxon, rule=1)
return assocparser.ParseResult(line, [], True)
if db_object_id == "":
self.report.error(line, Report.INVALID_ID, "EMPTY", "col2 is empty", taxon=taxon, rule=1)
return assocparser.ParseResult(line, [], True)
if taxon == "":
self.report.error(line, Report.INVALID_TAXON, "EMPTY", "taxon column is empty", taxon=taxon, rule=1)
return assocparser.ParseResult(line, [], True)
if reference == "":
self.report.error(line, Report.INVALID_ID, "EMPTY", "reference column 6 is empty", taxon=taxon, rule=1)
return assocparser.ParseResult(line, [], True)
## --
## db + db_object_id. CARD=1
## --
id = self._pair_to_id(db, db_object_id)
if not self._validate_id(id, split_line, ENTITY):
print("skipping because {} not validated!".format(id))
return assocparser.ParseResult(line, [], True)
# Using a given gpi file to validate the gene object
if self.gpi is not None:
entity = self.gpi.get(id, None)
if entity is not None:
db_object_symbol = entity["symbol"]
db_object_name = entity["name"]
db_object_synonym = entity["synonyms"]
db_object_type = entity["type"]
if not self._validate_id(goid, split_line, ANNOTATION):
print("skipping because {} not validated!".format(goid))
return assocparser.ParseResult(line, [], True)
valid_goid = self._validate_ontology_class_id(goid, split_line)
if valid_goid == None:
return assocparser.ParseResult(line, [], True)
goid = valid_goid
date = self._normalize_gaf_date(date, split_line)
if date == None:
return assocparser.ParseResult(line, [], True)
vals[13] = date
ecomap = self.config.ecomap
if ecomap is not None:
if ecomap.coderef_to_ecoclass(evidence, reference) is None:
self.report.error(line, assocparser.Report.UNKNOWN_EVIDENCE_CLASS, evidence,
msg="Expecting a known ECO GAF code, e.g ISS")
return assocparser.ParseResult(line, [], True)
# Throw out the line if it uses GO_REF:0000033, see https://github.com/geneontology/go-site/issues/563#event-1519351033
if "GO_REF:0000033" in reference.split("|"):
self.report.error(line, assocparser.Report.INVALID_ID, reference,
msg="Disallowing GO_REF:0000033 in reference field as of 03/13/2018")
return assocparser.ParseResult(line, [], True)
references = self.validate_pipe_separated_ids(reference, split_line)
if references == None:
# Reporting occurs in above function call
return assocparser.ParseResult(line, [], True)
# With/From
withfroms = self.validate_pipe_separated_ids(withfrom, split_line, empty_allowed=True, extra_delims=",")
if withfroms == None:
# Reporting occurs in above function call
return assocparser.ParseResult(line, [], True)
# validation
self._validate_symbol(db_object_symbol, split_line)
# Example use case: mapping from UniProtKB to MOD ID
if self.config.entity_map is not None:
id = self.map_id(id, self.config.entity_map)
toks = id.split(":")
db = toks[0]
db_object_id = toks[1:]
vals[1] = db_object_id
if goid.startswith("GO:") and aspect.upper() not in ["C", "F", "P"]:
self.report.error(line, assocparser.Report.INVALID_ASPECT, aspect)
return assocparser.ParseResult(line, [], True)
go_rule_results = qc.test_go_rules(vals, self.config)
for rule_id, result in go_rule_results.items():
if result.result_type == qc.ResultType.WARNING:
self.report.warning(line, assocparser.Report.VIOLATES_GO_RULE, goid,
msg="{id}: {message}".format(id=rule_id, message=result.message))
# Skip the annotation
return assocparser.ParseResult(line, [], True)
if result.result_type == qc.ResultType.ERROR:
self.report.error(line, assocparser.Report.VIOLATES_GO_RULE, goid,
msg="{id}: {message}".format(id=rule_id, message=result.message))
# Skip the annotation
return assocparser.ParseResult(line, [], True)
## --
## end of line re-processing
## --
# regenerate line post-mapping
line = "\t".join(vals)
## --
## taxon CARD={1,2}
## --
## if a second value is specified, this is the interacting taxon
## We do not use the second value
normalized_taxon = self._taxon_id(taxon.split("|")[0], split_line)
if normalized_taxon == None:
self.report.error(line, assocparser.Report.INVALID_TAXON, taxon,
msg="Taxon ID is invalid")
return assocparser.ParseResult(line, [], True)
self._validate_taxon(normalized_taxon, split_line)
## --
## db_object_synonym CARD=0..*
## --
synonyms = db_object_synonym.split("|")
if db_object_synonym == "":
synonyms = []
## --
## parse annotation extension
## See appendix in http://doi.org/10.1186/1471-2105-15-155
## --
object_or_exprs = self._parse_full_extension_expression(annotation_xp, line=split_line)
## --
## qualifier
## --
negated, relation, other_qualifiers = self._parse_qualifier(qualifier, aspect)
## --
## goid
## --
# TODO We shouldn't overload buildin keywords/functions
object = {'id': goid,
'taxon': normalized_taxon}
# construct subject dict
subject = {
'id': id,
'label': db_object_symbol,
'type': db_object_type,
'fullname': db_object_name,
'synonyms': synonyms,
'taxon': {
'id': normalized_taxon
}
}
## --
## gene_product_isoform
## --
## This is mapped to a more generic concept of subject_extensions
subject_extns = []
if gene_product_isoform is not None and gene_product_isoform != '':
subject_extns.append({'property':'isoform', 'filler':gene_product_isoform})
## --
## evidence
## reference
## withfrom
## --
evidence_obj = {
'type': evidence,
'has_supporting_reference': references,
'with_support_from': withfroms
}
## Construct main return dict
assoc = {
'source_line': line,
'subject': subject,
'object': object,
'negated': negated,
'qualifiers': other_qualifiers,
'aspect': aspect,
'relation': {
'id': relation
},
'evidence': evidence_obj,
'provided_by': assigned_by,
'date': date,
}
if len(subject_extns) > 0:
assoc['subject_extensions'] = subject_extns
if object_or_exprs is not None and len(object_or_exprs) > 0:
assoc['object_extensions'] = {'union_of': object_or_exprs}
return assocparser.ParseResult(line, [assoc], False, evidence.upper())
def parse_line(self, line):
"""
Parses a single line of a GAF
Return a tuple `(processed_line, associations)`. Typically
there will be a single association, but in some cases there
may be none (invalid line) or multiple (disjunctive clause in
annotation extensions)
Note: most applications will only need to call this directly if they require fine-grained control of parsing. For most purposes,
:method:`parse_file` can be used over the whole file
Arguments
---------
line : str
A single tab-seperated line from a GAF file
"""
# Returns assocparser.ParseResult
parsed = super().validate_line(line)
if parsed:
return parsed
if self.is_header(line):
# Save off version info here
if self.version is None:
# We are still looking
parsed = parser_version_regex.findall(line)
if len(parsed) == 1:
filetype, version, _ = parsed[0]
if version == "2.2":
logger.info("Detected GAF version 2.2")
self.version = version
else:
logger.info("Detected GAF version {}, so using 2.1".format(version))
self.version = self.default_version
# Compute the cell component subclass closure
self.make_internal_cell_component_closure()
return assocparser.ParseResult(line, [{ "header": True, "line": line.strip() }], False)
# At this point, we should have gone through all the header, and a version number should be established
if self.version is None:
logger.warning("No version number found for this file so we will assume GAF version: {}".format(self.default_version))
self.version = self.default_version
self.make_internal_cell_component_closure()
vals = [el.strip() for el in line.split("\t")]
# GAF v1 is defined as 15 cols, GAF v2 as 17.
# We treat everything as GAF2 by adding two blank columns.
# TODO: check header metadata to see if columns corresponds to declared dataformat version
parsed = to_association(list(vals), report=self.report, qualifier_parser=self.qualifier_parser(), bio_entities=self.bio_entities)
if parsed.associations == []:
return parsed
assoc = parsed.associations[0]
# Qualifier is index 3
# If we are 2.1, and qualifier has no relation
# Also must have an ontology
# Then upgrade
# For https://github.com/geneontology/go-site/issues/1558
if self.gaf_version() == "2.1" and (vals[3] == "" or vals[3] == "NOT") and self.config.ontology:
assoc = self.upgrade_empty_qualifier(assoc)
## Run GO Rules, save split values into individual variables
# print("Config is {}".format(self.config.__dict__.keys()))
go_rule_results = qc.test_go_rules(assoc, self.config, group=self.group)
for rule, result in go_rule_results.all_results.items():
if result.result_type == qc.ResultType.WARNING:
self.report.warning(line, assocparser.Report.VIOLATES_GO_RULE, "",
msg="{id}: {message}".format(id=rule.id, message=result.message), rule=int(rule.id.split(":")[1]))
if result.result_type == qc.ResultType.ERROR:
self.report.error(line, assocparser.Report.VIOLATES_GO_RULE, "",
msg="{id}: {message}".format(id=rule.id, message=result.message), rule=int(rule.id.split(":")[1]))
# Skip the annotation
return assocparser.ParseResult(line, [], True)
if result.result_type == qc.ResultType.PASS:
self.report.message(assocparser.Report.INFO, line, Report.RULE_PASS, "",
msg="Passing Rule", rule=int(rule.id.split(":")[1]))
assoc = go_rule_results.annotation # type: association.GoAssociation
split_line = assocparser.SplitLine(line=line, values=vals, taxon=str(assoc.object.taxon))
if self.config.group_idspace is not None and assoc.provided_by not in self.config.group_idspace:
self.report.warning(line, Report.INVALID_ID, assoc.provided_by,
"GORULE:0000027: assigned_by is not present in groups reference", taxon=str(assoc.object.taxon), rule=27)
db = assoc.subject.id.namespace
if self.config.entity_idspaces is not None and db not in self.config.entity_idspaces:
# Are we a synonym?
upgrade = self.config.entity_idspaces.reverse(db)
if upgrade is not None:
# If we found a synonym
self.report.warning(line, Report.INVALID_ID_DBXREF, db, "GORULE:0000027: {} is a synonym for the correct ID {}, and has been updated".format(db, upgrade), taxon=str(assoc.object.taxon), rule=27)
assoc.subject.id.namespace = upgrade
## --
## db + db_object_id. CARD=1
## --assigned_by
if not self._validate_id(str(assoc.subject.id), split_line, allowed_ids=self.config.entity_idspaces):
return assocparser.ParseResult(line, [], True)
# Using a given gpi file to validate the gene object
# if self.gpi is not None:
# entity = self.gpi.get(str(assoc.subject.id), None)
# if entity is not None:
# assoc.subject.label = entity["symbol"]
# assoc.subject.fullname = entity["name"]
# assoc.subject.synonyms = entity["synonyms"].split("|")
# assoc.subject.type = entity["type"]
if not self._validate_id(str(assoc.object.id), split_line, context=ANNOTATION):
print("skipping because {} not validated!".format(assoc.object.id))
return assocparser.ParseResult(line, [], True)
valid_goid = self._validate_ontology_class_id(str(assoc.object.id), split_line)
if valid_goid is None:
return assocparser.ParseResult(line, [], True)
assoc.object.id = association.Curie.from_str(valid_goid)
references = self.validate_curie_ids(assoc.evidence.has_supporting_reference, split_line)
if references is None:
# Reporting occurs in above function call
return assocparser.ParseResult(line, [], True)
# With/From
for wf in assoc.evidence.with_support_from:
validated = self.validate_curie_ids(wf.elements, split_line)
if validated is None:
return assocparser.ParseResult(line, [], True)
with_support_from = self._unroll_withfrom_and_replair_obsoletes(split_line, 'gaf')
if with_support_from is None:
return assocparser.ParseResult(line, [], True)
assoc.evidence.with_support_from = with_support_from
# validation
self._validate_symbol(assoc.subject.label, split_line)
## --
## taxon CARD={1,2}
## --
## if a second value is specified, this is the interacting taxon
## We do not use the second value
valid_taxon = self._validate_taxon(str(assoc.object.taxon), split_line)
valid_interacting = self._validate_taxon(str(assoc.interacting_taxon), split_line) if assoc.interacting_taxon else True
if not valid_taxon:
self.report.error(line, assocparser.Report.INVALID_TAXON, str(assoc.object.taxon), "Taxon ID is invalid", rule=27)
if not valid_interacting:
self.report.error(line, assocparser.Report.INVALID_TAXON, str(assoc.interacting_taxon), "Taxon ID is invalid", rule=27)
if (not valid_taxon) or (not valid_interacting):
return assocparser.ParseResult(line, [], True)
return assocparser.ParseResult(line, [assoc], False, vals[6])
def parse_line(self, line):
"""Parses a single line of a GPAD.
Return a tuple `(processed_line, associations)`. Typically
there will be a single association, but in some cases there
may be none (invalid line) or multiple (disjunctive clause in
annotation extensions)
Note: most applications will only need to call this directly if they require fine-grained control of parsing. For most purposes,
:method:`parse_file` can be used over the whole file
Arguments
---------
line : str
A single tab-seperated line from a GPAD file
"""
parsed = super().validate_line(line)
if parsed:
return parsed
if self.is_header(line):
if self.version is None:
# We are still looking
parsed = parser_version_regex.findall(line)
if len(parsed) == 1:
filetype, version, _ = parsed[0]
if version == "2.0":
logger.info("Detected GPAD version 2.0")
self.version = version
else:
logger.info(
"Detected GPAD version {}, so defaulting to 1.2".
format(version))
self.version = self.default_version
return assocparser.ParseResult(line, [{
"header": True,
"line": line.strip()
}], False)
# At this point, we should have gone through all the header, and a version number should be established
if self.version is None:
logger.warning(
"No version number found for this file so we will assume GPAD version: {}"
.format(self.default_version))
self.version = self.default_version
vals = [el.strip() for el in line.split("\t")]
parsed = to_association(list(vals),
report=self.report,
version=self.gpad_version(),
bio_entities=self.bio_entities)
if parsed.associations == []:
return parsed
assoc = parsed.associations[0]
go_rule_results = qc.test_go_rules(assoc, self.config)
for rule, result in go_rule_results.all_results.items():
if result.result_type == qc.ResultType.WARNING:
self.report.warning(line,
assocparser.Report.VIOLATES_GO_RULE,
"",
msg="{id}: {message}".format(
id=rule.id, message=result.message),
rule=int(rule.id.split(":")[1]))
if result.result_type == qc.ResultType.ERROR:
self.report.error(line,
assocparser.Report.VIOLATES_GO_RULE,
"",
msg="{id}: {message}".format(
id=rule.id, message=result.message),
rule=int(rule.id.split(":")[1]))
# Skip the annotation
return assocparser.ParseResult(line, [], True)
if result.result_type == qc.ResultType.PASS:
self.report.message(assocparser.Report.INFO,
line,
Report.RULE_PASS,
"",
msg="Passing Rule",
rule=int(rule.id.split(":")[1]))
assoc = go_rule_results.annotation # type: association.GoAssociation
split_line = assocparser.SplitLine(line=line, values=vals, taxon="")
if not self._validate_id(
str(assoc.subject.id), split_line, context=ENTITY):
return assocparser.ParseResult(line, [], True)
if not self._validate_id(
str(assoc.object.id), split_line, context=ANNOTATION):
return assocparser.ParseResult(line, [], True)
valid_goid = self._validate_ontology_class_id(str(assoc.object.id),
split_line)
if valid_goid is None:
return assocparser.ParseResult(line, [], True)
assoc.object.id = association.Curie.from_str(valid_goid)
if not self._validate_id(str(assoc.evidence.type), split_line):
return assocparser.ParseResult(line, [], True)
if assoc.interacting_taxon:
if not self._validate_taxon(str(assoc.interacting_taxon),
split_line):
self.report.error(line,
assocparser.Report.INVALID_TAXON,
str(assoc.interacting_taxon),
"Taxon ID is invalid",
rule=27)
return assocparser.ParseResult(line, [], True)
#TODO: ecomap is currently one-way only
#ecomap = self.config.ecomap
#if ecomap != None:
# if ecomap.ecoclass_to_coderef(evidence) == (None,None):
# self.report.error(line, Report.UNKNOWN_EVIDENCE_CLASS, evidence,
# msg="Expecting a known ECO class ID")
# Reference Column
references = self.validate_curie_ids(
assoc.evidence.has_supporting_reference, split_line)
if references is None:
return assocparser.ParseResult(line, [], True)
# With/From
for wf in assoc.evidence.with_support_from:
validated = self.validate_curie_ids(wf.elements, split_line)
if validated is None:
return assocparser.ParseResult(line, [], True)
return assocparser.ParseResult(line, [assoc], False)
def parse_line(self, line):
"""
Parses a single line of a GAF
Return a tuple `(processed_line, associations)`. Typically
there will be a single association, but in some cases there
may be none (invalid line) or multiple (disjunctive clause in
annotation extensions)
Note: most applications will only need to call this directly if they require fine-grained control of parsing. For most purposes,
:method:`parse_file` can be used over the whole file
Arguments
---------
line : str
A single tab-seperated line from a GAF file
"""
# Returns assocparser.ParseResult
parsed = super().validate_line(line)
if parsed:
return parsed
if self.is_header(line):
return assocparser.ParseResult(line, [{
"header": True,
"line": line.strip()
}], False)
vals = [el.strip() for el in line.split("\t")]
# GAF v1 is defined as 15 cols, GAF v2 as 17.
# We treat everything as GAF2 by adding two blank columns.
# TODO: check header metadata to see if columns corresponds to declared dataformat version
parsed = to_association(list(vals), report=self.report)
if parsed.associations == []:
return parsed
assoc = parsed.associations[0]
# self.report = parsed.report
## Run GO Rules, save split values into individual variables
go_rule_results = qc.test_go_rules(assoc,
self.config,
group=self.group)
for rule, result in go_rule_results.all_results.items():
if result.result_type == qc.ResultType.WARNING:
self.report.warning(line,
assocparser.Report.VIOLATES_GO_RULE,
"",
msg="{id}: {message}".format(
id=rule.id, message=result.message),
rule=int(rule.id.split(":")[1]))
if result.result_type == qc.ResultType.ERROR:
self.report.error(line,
assocparser.Report.VIOLATES_GO_RULE,
"",
msg="{id}: {message}".format(
id=rule.id, message=result.message),
rule=int(rule.id.split(":")[1]))
# Skip the annotation
return assocparser.ParseResult(line, [], True)
if result.result_type == qc.ResultType.PASS:
self.report.message(assocparser.Report.INFO,
line,
Report.RULE_PASS,
"",
msg="Passing Rule",
rule=int(rule.id.split(":")[1]))
vals = list(go_rule_results.annotation.to_gaf_tsv())
[
db, db_object_id, db_object_symbol, qualifier, goid, reference,
evidence, withfrom, aspect, db_object_name, db_object_synonym,
db_object_type, taxon, date, assigned_by, annotation_xp,
gene_product_isoform
] = vals
split_line = assocparser.SplitLine(line=line, values=vals, taxon=taxon)
if self.config.group_idspace is not None and assigned_by not in self.config.group_idspace:
self.report.warning(
line,
Report.INVALID_ID,
assigned_by,
"GORULE:0000027: assigned_by is not present in groups reference",
taxon=taxon,
rule=27)
if self.config.entity_idspaces is not None and db not in self.config.entity_idspaces:
# Are we a synonym?
upgrade = self.config.entity_idspaces.reverse(db)
if upgrade is not None:
# If we found a synonym
self.report.warning(
line,
Report.INVALID_ID_DBXREF,
db,
"GORULE:0000027: {} is a synonym for the correct ID {}, and has been updated"
.format(db, upgrade),
taxon=taxon,
rule=27)
db = upgrade
## --
## db + db_object_id. CARD=1
## --
id = self._pair_to_id(db, db_object_id)
if not self._validate_id(
id, split_line, allowed_ids=self.config.entity_idspaces):
return assocparser.ParseResult(line, [], True)
# Using a given gpi file to validate the gene object
if self.gpi is not None:
entity = self.gpi.get(id, None)
if entity is not None:
db_object_symbol = entity["symbol"]
db_object_name = entity["name"]
db_object_synonym = entity["synonyms"]
db_object_type = entity["type"]
if not self._validate_id(goid, split_line, context=ANNOTATION):
print("skipping because {} not validated!".format(goid))
return assocparser.ParseResult(line, [], True)
valid_goid = self._validate_ontology_class_id(goid, split_line)
if valid_goid == None:
return assocparser.ParseResult(line, [], True)
goid = valid_goid
date = self._normalize_gaf_date(date, split_line)
if date == None:
return assocparser.ParseResult(line, [], True)
vals[13] = date
ecomap = self.config.ecomap
if ecomap is not None:
if ecomap.coderef_to_ecoclass(evidence, reference) is None:
self.report.error(
line,
assocparser.Report.UNKNOWN_EVIDENCE_CLASS,
evidence,
msg="Expecting a known ECO GAF code, e.g ISS",
rule=1)
return assocparser.ParseResult(line, [], True)
references = self.validate_pipe_separated_ids(reference, split_line)
if references == None:
# Reporting occurs in above function call
return assocparser.ParseResult(line, [], True)
# With/From
withfroms = self.validate_pipe_separated_ids(withfrom,
split_line,
empty_allowed=True,
extra_delims=",")
if withfroms == None:
# Reporting occurs in above function call
return assocparser.ParseResult(line, [], True)
# validation
self._validate_symbol(db_object_symbol, split_line)
# Example use case: mapping from UniProtKB to MOD ID
if self.config.entity_map is not None:
id = self.map_id(id, self.config.entity_map)
toks = id.split(":")
db = toks[0]
db_object_id = toks[1:]
vals[1] = db_object_id
## --
## end of line re-processing
## --
# regenerate line post-mapping
line = "\t".join(vals)
## --
## taxon CARD={1,2}
## --
## if a second value is specified, this is the interacting taxon
## We do not use the second value
taxons = taxon.split("|")
normalized_taxon = self._taxon_id(taxons[0], split_line)
if normalized_taxon == None:
self.report.error(line,
assocparser.Report.INVALID_TAXON,
taxon,
msg="Taxon ID is invalid")
return assocparser.ParseResult(line, [], True)
self._validate_taxon(normalized_taxon, split_line)
interacting_taxon = None
if len(taxons) == 2:
interacting_taxon = self._taxon_id(taxons[1], split_line)
if interacting_taxon == None:
self.report.error(line,
assocparser.Report.INVALID_TAXON,
taxon,
msg="Taxon ID is invalid")
return assocparser.ParseResult(line, [], True)
## --
## db_object_synonym CARD=0..*
## --
synonyms = db_object_synonym.split("|")
if db_object_synonym == "":
synonyms = []
## --
## parse annotation extension
## See appendix in http://doi.org/10.1186/1471-2105-15-155
## --
object_or_exprs = self._parse_full_extension_expression(
annotation_xp, line=split_line)
## --
## qualifier
## --
negated, relation, other_qualifiers = self._parse_qualifier(
qualifier, aspect)
## --
## goid
## --
# TODO We shouldn't overload buildin keywords/functions
object = {'id': goid, 'taxon': normalized_taxon}
# construct subject dict
subject = {
'id': id,
'label': db_object_symbol,
'type': db_object_type,
'fullname': db_object_name,
'synonyms': synonyms,
'taxon': {
'id': normalized_taxon
}
}
## --
## gene_product_isoform
## --
## This is mapped to a more generic concept of subject_extensions
subject_extns = []
if gene_product_isoform is not None and gene_product_isoform != '':
subject_extns.append({
'property': 'isoform',
'filler': gene_product_isoform
})
object_extensions = {}
if object_or_exprs is not None and len(object_or_exprs) > 0:
object_extensions['union_of'] = object_or_exprs
## --
## evidence
## reference
## withfrom
## --
evidence_obj = {
'type': evidence,
'has_supporting_reference': references,
'with_support_from': withfroms
}
## Construct main return dict
assoc = {
'source_line': line,
'subject': subject,
'object': object,
'negated': negated,
'qualifiers': other_qualifiers,
'aspect': aspect,
'relation': {
'id': relation
},
'interacting_taxon': interacting_taxon,
'evidence': evidence_obj,
'provided_by': assigned_by,
'date': date,
'subject_extensions': subject_extns,
'object_extensions': object_extensions
}
return assocparser.ParseResult(line, [assoc], False, evidence.upper())
def parse_line(self, line):
"""Parses a single line of a GPAD.
Return a tuple `(processed_line, associations)`. Typically
there will be a single association, but in some cases there
may be none (invalid line) or multiple (disjunctive clause in
annotation extensions)
Note: most applications will only need to call this directly if they require fine-grained control of parsing. For most purposes,
:method:`parse_file` can be used over the whole file
Arguments
---------
line : str
A single tab-seperated line from a GPAD file
"""
parsed = super().validate_line(line)
if parsed:
return parsed
if self.is_header(line):
return assocparser.ParseResult(line, [{
"header": True,
"line": line.strip()
}], False)
vals = [el.strip() for el in line.split("\t")]
parsed = to_association(list(vals), report=self.report)
if parsed.associations == []:
return parsed
assoc = parsed.associations[0]
go_rule_results = qc.test_go_rules(assoc, self.config)
for rule, result in go_rule_results.all_results.items():
if result.result_type == qc.ResultType.WARNING:
self.report.warning(line,
assocparser.Report.VIOLATES_GO_RULE,
"",
msg="{id}: {message}".format(
id=rule.id, message=result.message),
rule=int(rule.id.split(":")[1]))
if result.result_type == qc.ResultType.ERROR:
self.report.error(line,
assocparser.Report.VIOLATES_GO_RULE,
"",
msg="{id}: {message}".format(
id=rule.id, message=result.message),
rule=int(rule.id.split(":")[1]))
# Skip the annotation
return assocparser.ParseResult(line, [], True)
if result.result_type == qc.ResultType.PASS:
self.report.message(assocparser.Report.INFO,
line,
Report.RULE_PASS,
"",
msg="Passing Rule",
rule=int(rule.id.split(":")[1]))
vals = list(go_rule_results.annotation.to_gpad_tsv())
[
db, db_object_id, qualifier, goid, reference, evidence, withfrom,
interacting_taxon_id, date, assigned_by, annotation_xp,
annotation_properties
] = vals
split_line = assocparser.SplitLine(line=line, values=vals, taxon="")
id = self._pair_to_id(db, db_object_id)
if not self._validate_id(id, split_line, context=ENTITY):
return assocparser.ParseResult(line, [], True)
if not self._validate_id(goid, split_line, context=ANNOTATION):
return assocparser.ParseResult(line, [], True)
valid_goid = self._validate_ontology_class_id(goid, split_line)
if valid_goid == None:
return assocparser.ParseResult(line, [], True)
goid = valid_goid
date = self._normalize_gaf_date(date, split_line)
if reference == "":
self.report.error(line, Report.INVALID_ID, "EMPTY",
"reference column 6 is empty")
return assocparser.ParseResult(line, [], True)
self._validate_id(evidence, split_line)
interacting_taxon = None if interacting_taxon_id == "" else interacting_taxon_id
if interacting_taxon != None:
interacting_taxon = self._taxon_id(interacting_taxon_id,
split_line)
if interacting_taxon == None:
self.report.error(line,
assocparser.Report.INVALID_TAXON,
interacting_taxon_id,
msg="Taxon ID is invalid")
return assocparser.ParseResult(line, [], True)
#TODO: ecomap is currently one-way only
#ecomap = self.config.ecomap
#if ecomap != None:
# if ecomap.ecoclass_to_coderef(evidence) == (None,None):
# self.report.error(line, Report.UNKNOWN_EVIDENCE_CLASS, evidence,
# msg="Expecting a known ECO class ID")
## --
## qualifier
## --
negated, relation, other_qualifiers = self._parse_qualifier(
qualifier, None)
# Reference Column
references = self.validate_pipe_separated_ids(reference, split_line)
if references == None:
# Reporting occurs in above function call
return assocparser.ParseResult(line, [], True)
# With/From
withfroms = self.validate_pipe_separated_ids(withfrom,
split_line,
empty_allowed=True,
extra_delims=",")
if withfroms == None:
# Reporting occurs in above function call
return assocparser.ParseResult(line, [], True)
## --
## parse annotation extension
## See appending in http://doi.org/10.1186/1471-2105-15-155
## --
object_or_exprs = self._parse_full_extension_expression(
annotation_xp, line=split_line)
subject_symbol = id
subject_fullname = id
subject_synonyms = []
if self.gpi is not None:
gp = self.gpi.get(id, {})
if gp is not {}:
subject_symbol = gp["symbol"]
subject_fullname = gp["name"]
subject_synonyms = gp["synonyms"].split("|")
assoc = {
'source_line': line,
'subject': {
'id': id,
'label': subject_symbol,
'fullname': subject_fullname,
'synonyms': subject_synonyms,
'taxon': {
'id': interacting_taxon
},
},
'object': {
'id': goid
},
'negated': negated,
'relation': {
'id': relation
},
'interacting_taxon': interacting_taxon,
'evidence': {
'type': evidence,
'with_support_from': withfroms,
'has_supporting_reference': references
},
'subject_extensions': [],
'object_extensions': {},
'aspect': self.compute_aspect(goid),
'provided_by': assigned_by,
'date': date,
}
if len(other_qualifiers) > 0:
assoc['qualifiers'] = other_qualifiers
if object_or_exprs is not None and len(object_or_exprs) > 0:
assoc['object_extensions'] = {'union_of': object_or_exprs}
return assocparser.ParseResult(line, [assoc], False)
