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 create_parser_from_header(
line: str,
config: assocparser.AssocParserConfig,
group="unknown",
dataset="unknown",
bio_entities=None) -> Optional[assocparser.AssocParser]:
parser = None
parsed_version = parser_version_regex.findall(line)
if len(parsed_version) == 1:
filetype, version, _ = parsed_version[0]
if filetype in ["gpad", "gpa"]:
parser = gpadparser.GpadParser(config=config,
bio_entities=bio_entities,
group=group,
dataset=dataset)
if version in ["1.2", "2.0"]:
parser.version = version
elif filetype == "gaf":
parser = gafparser.GafParser(config=config,
bio_entities=bio_entities,
group=group,
dataset=dataset)
if version in ["2.1", "2.2"]:
parser.version = version
return parser
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_writing_assoc_properties():
line = "MGI:MGI:1922721\t\tRO:0002327\tGO:0019904\tMGI:MGI:3769586|PMID:17984326\tECO:0000353\tPR:Q0KK55\t\t2010-12-01\tMGI\tBFO:0000066(EMAPA:17787),RO:0002233(MGI:MGI:1923734)\tcreation-date=2008-02-07|modification-date=2010-12-01|comment=v-KIND domain binding of Kndc1;MGI:1923734|contributor-id=http://orcid.org/0000-0003-2689-5511|contributor-id=http://orcid.org/0000-0003-3394-9805"
parser = gpadparser.GpadParser()
parser.version = "2.0"
out = io.StringIO()
writer = assocwriter.GpadWriter(
file=out, version="2.0") # Write back out to gpad 2.0
assoc = parser.parse_line(line).associations[0]
writer.write_assoc(assoc)
written_gpad_line = [
line for line in out.getvalue().split("\n") if not line.startswith("!")
][0]
written_props = written_gpad_line.split("\t")[11]
assert len(written_props.split("|")) == 5
def __init__(self, gpad_file, parser_config: AssocParserConfig):
self.assocs = []
self.gpad_parser = gpadparser.GpadParser(config=parser_config)
with open(gpad_file) as sg:
lines = sum(1 for line in sg)
with open(gpad_file) as gf:
click.echo("Making products...")
with click.progressbar(
iterable=self.gpad_parser.association_generator(
file=gf, skipheader=True),
length=lines) as associations:
self.assocs = list(associations)
self.entity_parents = self.parse_gpi_parents(
parser_config.gpi_authority_path)
def read_gpad_csv(filename, version) -> pd:
if version.startswith("1"):
data_frame = pd.read_csv(filename,
comment='!',
sep='\t',
header=None,
na_filter=False,
names=gpad_1_2_format).fillna("")
df = data_frame.filter(['db', 'subject', 'qualifiers', 'relation', 'object', 'evidence_code', 'reference'], axis=1)
concat_column = df['db'] + ":" + df['subject']
df['concat_column'] = concat_column
filtered_df = df.filter(['concat_column', 'qualifiers', 'relation', 'object', 'evidence_code', 'reference'])
filtered_df.rename(columns={'concat_column': 'subject'}, inplace=True)
new_df = filtered_df
else:
data_frame = pd.read_csv(filename,
comment='!',
sep='\t',
header=None,
na_filter=False,
names=gpad_2_0_format).fillna("")
new_df = data_frame.filter(['subject', 'negation', 'relation', 'object', 'evidence_code', 'reference'], axis=1)
ecomapping = ecomap.EcoMap()
for eco_code in ecomapping.mappings():
for ev in new_df['evidence_code']:
if eco_code[2] == ev:
new_df['evidence_code'] = new_df['evidence_code'].replace([eco_code[2]],
ecomapping.ecoclass_to_coderef(eco_code[2])[0])
# normalize ids
config = assocparser.AssocParserConfig()
config.remove_double_prefixes = True
parser = gpadparser.GpadParser(config=config)
for i, r in enumerate(new_df['subject']):
r1 = parser._normalize_id(r)
new_df.at[i, 'subject'] = r1
return new_df
