def test_roundtrip():
"""
Start with a line, parse it, then write it. The beginning line should be the same as what was written.
"""
line = "PomBase\tSPAC25B8.17\typf1\t\tGO:0000006\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:999|taxon:888\t20150305\tPomBase\tfoo(X:1)\tUniProtKB:P12345"
parser = gafparser.GafParser()
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
assoc_dict = parser.parse_line(line).associations[0]
writer.write_assoc(assoc_dict)
gaf = [
line for line in out.getvalue().split("\n") if not line.startswith("!")
][0]
assert line == gaf
# Single taxon
line = "PomBase\tSPAC25B8.17\typf1\t\tGO:0000006\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:1111\t20150305\tPomBase\tfoo(X:1)\tUniProtKB:P12345"
parser = gafparser.GafParser()
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
assoc_dict = parser.parse_line(line).associations[0]
writer.write_assoc(assoc_dict)
gaf = [
line for line in out.getvalue().split("\n") if not line.startswith("!")
][0]
assert line == gaf
def test_gaf2_2_qualifier_to_gaf2_1():
# Qualifier is `part_of` and should be returned blank instead of removing the whole line
line = "WB\tWBGene00000001\taap-1\tinvolved_in\tGO:0008286\tWB_REF:WBPaper00005614|PMID:12393910\tIMP\t\tP\t\tY110A7A.10\tgene\ttaxon:6239\t20060302\tWB\t\t"
parser = gafparser.GafParser()
parser.version = "2.2"
out = io.StringIO()
writer = assocwriter.GafWriter(file=out,
version="2.1") # Write out to gaf 2.1
assoc = parser.parse_line(line).associations[0]
writer.write_assoc(assoc)
gpad_to_gaf_line = [
line for line in out.getvalue().split("\n") if not line.startswith("!")
][0]
assert gpad_to_gaf_line.split("\t")[3] == ""
# Test with a `NOT`
line = "WB\tWBGene00000001\taap-1\tNOT|involved_in\tGO:0008286\tWB_REF:WBPaper00005614|PMID:12393910\tIMP\t\tP\t\tY110A7A.10\tgene\ttaxon:6239\t20060302\tWB\t\t"
parser = gafparser.GafParser()
parser.version = "2.2"
out = io.StringIO()
writer = assocwriter.GafWriter(file=out,
version="2.1") # Write out to gaf 2.1
assoc = parser.parse_line(line).associations[0]
writer.write_assoc(assoc)
gpad_to_gaf_line = [
line for line in out.getvalue().split("\n") if not line.startswith("!")
][0]
assert gpad_to_gaf_line.split("\t")[3] == "NOT"
def test_gpad_qualifier_removed_in_gaf_2_1():
# Qualifier is `part_of` and should be returned blank instead of removing the whole line
line = "PomBase\tSPBC1348.01\tpart_of\tGO:0009897\tGO_REF:0000051\tECO:0000266\t\t\t20060201\tPomBase\t\t"
parser = gpadparser.GpadParser()
out = io.StringIO()
writer = assocwriter.GafWriter(file=out,
version="2.1") # Write out to gaf 2.1
assoc = parser.parse_line(line).associations[0]
writer.write_assoc(assoc)
gpad_to_gaf_line = [
line for line in out.getvalue().split("\n") if not line.startswith("!")
][0]
assert gpad_to_gaf_line.split("\t")[3] == ""
# Test with a `NOT`
line = "PomBase\tSPBC1348.01\tNOT|part_of\tGO:0009897\tGO_REF:0000051\tECO:0000266\t\t\t20060201\tPomBase\t\t"
parser = gpadparser.GpadParser()
out = io.StringIO()
writer = assocwriter.GafWriter(file=out,
version="2.1") # Write out to gaf 2.1
assoc = parser.parse_line(line).associations[0]
writer.write_assoc(assoc)
gpad_to_gaf_line = [
line for line in out.getvalue().split("\n") if not line.startswith("!")
][0]
assert gpad_to_gaf_line.split("\t")[3] == "NOT"
def parse_gpad_vals_to_gaf_io(gpad_vals):
parser = gpadparser.GpadParser()
gaf_out = io.StringIO()
writer = assocwriter.GafWriter(file=gaf_out)
assoc = parser.parse_line("\t".join(gpad_vals)).associations[0]
writer.write_assoc(assoc)
return gaf_out
def test_gaf_writer():
association = {
"subject": {
"id": "PomBase:SPAC25B8.17",
"label": "ypf1",
"type": "protein",
"fullname":
"intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)",
"synonyms": ["ppp81"],
"taxon": {
"id": "NCBITaxon:4896"
}
},
"object": {
"id": "GO:0000006",
"taxon": "NCBITaxon:4896"
},
"negated":
False,
"qualifiers": [],
"aspect":
"C",
"relation": {
"id": "part_of"
},
"interacting_taxon":
"NCBITaxon:555",
"evidence": {
"type": "ISO",
"has_supporting_reference": ["GO_REF:0000024"],
"with_support_from": ["SGD:S000001583"]
},
"provided_by":
"PomBase",
"date":
"20150305",
"subject_extensions": [{
"property": "isoform",
"filler": "UniProtKB:P12345"
}],
"object_extensions": {
"union_of": [{
"intersection_of": [{
"property": "foo",
"filler": "X:1"
}]
}]
}
}
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
expected = "PomBase\tSPAC25B8.17\typf1\t\tGO:0000006\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896|taxon:555\t20150305\tPomBase\tfoo(X:1)\tUniProtKB:P12345"
writer.write_assoc(association)
gaf = [
line for line in out.getvalue().split("\n") if not line.startswith("!")
][0]
assert expected == gaf
def test_full_gaf_2_2_write():
line = "WB\tWBGene00000001\taap-1\tinvolved_in\tGO:0008286\tWB_REF:WBPaper00005614|PMID:12393910\tIMP\t\tP\t\tY110A7A.10\tgene\ttaxon:6239\t20060302\tWB\t\t"
parser = gafparser.GafParser()
parser.version = "2.2"
out = io.StringIO()
writer = assocwriter.GafWriter(file=out, version="2.2")
assoc = parser.parse_line(line).associations[0]
writer.write_assoc(assoc)
out_line = [
line for line in out.getvalue().split("\n") if not line.startswith("!")
][0]
assert out_line.split("\t") == line.split("\t")
def test_gaf_writer():
association = GoAssociation(
source_line="",
subject=Subject(
id=Curie("PomBase", "SPAC25B8.17"),
label="ypf1",
type=["protein"],
fullname=[
"intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)"
],
synonyms=["ppp81"],
taxon=Curie("NCBITaxon", "4896")),
object=Term(id=Curie("GO", "0000006"),
taxon=Curie("NCBITaxon", "4896")),
negated=False,
qualifiers=[],
aspect=Aspect("C"),
relation=Curie("BFO", "0000050"),
interacting_taxon=Curie("NCBITaxon", "555"),
evidence=Evidence(
type=Curie("ECO", "0000266"),
has_supporting_reference=[Curie("GO_REF", "0000024")],
with_support_from=[
ConjunctiveSet(elements=[Curie("SGD", "S000001583")])
]),
provided_by=Provider("PomBase"),
date=Date(year="2015", month="03", day="05", time=""),
subject_extensions=[
ExtensionUnit(relation=Curie("rdfs", "subClassOf"),
term=Curie("UniProtKB", "P12345"))
],
object_extensions=[
ConjunctiveSet(elements=[
ExtensionUnit(relation=Curie("BFO", "0000050"),
term=Curie("X", "1"))
])
],
properties=dict())
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
# `out` will get written with gaf lines from the above assocation object
expected = "PomBase\tSPAC25B8.17\typf1\t\tGO:0000006\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896|taxon:555\t20150305\tPomBase\tpart_of(X:1)\tUniProtKB:P12345"
writer.write_assoc(association)
print(out.getvalue())
gaf = [
line.strip("\n") for line in out.getvalue().split("\n")
if not line.startswith("!")
][0]
assert expected == gaf
def test_single_entry_extension():
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
expression = {
"union_of": [{
"intersection_of": [{
"property": "foo",
"filler": "X:1"
}]
}]
}
extension = writer._extension_expression(expression)
assert "foo(X:1)" == extension
def validate_input(example: RuleExample, parser: assocparser.AssocParser, config=None) -> Parsed:
if config:
parser.config = config
out = []
writer = assocwriter.GafWriter(file=io.StringIO())
assocs_gen = parser.association_generator(file=io.StringIO(example.input), skipheader=True)
for assoc in assocs_gen:
out.append(writer.tsv_as_string(writer.as_tsv(assoc)))
rule_messages = parser.report.reporter.messages.get(example.rule_id, [])
rule_messages.extend(parser.report.reporter.messages.get("gorule-0000001", []))
# We have to also parse the expected result if we are in a repair to normalize all the data
expected_out = []
if example.example_type == ExampleType.REPAIR:
expected_parsed_gen = create_base_parser(example.format).association_generator(file=io.StringIO(example.expected), skipheader=True)
expected_writer = assocwriter.GafWriter(file=io.StringIO())
for assoc in expected_parsed_gen:
expected_out.append(expected_writer.tsv_as_string(expected_writer.as_tsv(assoc)))
# We only collect the messages from *our* rule we're in
return Parsed(report=rule_messages, output="\n".join(out), expected="\n".join(expected_out))
def test_negated_qualifers():
gaf = [
"PomBase", "SPBC11B10.09", "cdc2", "NOT", "GO:0007275",
"PMID:21873635", "ISO", "PANTHER:PTN000623979|TAIR:locus:2099478", "P",
"Cyclin-dependent kinase 1", "UniProtKB:P04551|PTN000624043",
"protein", "taxon:284812", "20170228", "GO_Central", "", ""
]
parser = gafparser.GafParser()
result = parser.parse_line("\t".join(gaf))
writer = assocwriter.GafWriter()
parsed = writer.as_tsv(result.associations[0])
print(parsed)
assert parsed[3] == "NOT"
writer = assocwriter.GpadWriter()
parsed = writer.as_tsv(result.associations[0])
print(parsed)
assert parsed[2] == "NOT|involved_in"
def test_intersection_extensions():
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
expression = {
"union_of": [{
"intersection_of": [{
"property": "foo",
"filler": "X:1"
}, {
"property": "foo",
"filler": "X:2"
}]
}, {
"intersection_of": [{
"property": "bar",
"filler": "Y:1"
}]
}]
}
extension = writer._extension_expression(expression)
assert "foo(X:1),foo(X:2)|bar(Y:1)" == extension
def test_empty_extension_expression():
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
extension = writer._extension_expression({})
assert extension == ""
def test_full_taxon_empty_string_interacting_taxon():
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
taxon_field = writer._full_taxon_field("taxon:12345", "")
assert "taxon:12345" == taxon_field
def test_full_taxon_field_interacting():
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
taxon_field = writer._full_taxon_field("taxon:12345", "taxon:6789")
assert "taxon:12345|taxon:6789" == taxon_field
def test_full_taxon_field_single_taxon():
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
taxon_field = writer._full_taxon_field("taxon:12345", None)
assert "taxon:12345" == taxon_field
