def test_parse(self):
"""
Runs WormBase.parse() and outputs dot file for each allele
This is less of a unit test and more for viewing the
output of an entire run on a single allele,
dot files can be converted to images using
scripts/dot-to-svg.sh
"""
for variant in VARIANTS:
with self.subTest(variant_id=variant):
self.tearDownAndSetUp()
self.gwascatalog.rawdir = RAW_PATH + '/' + variant
self.gwascatalog.parse()
dot_file_path = DOT_PATH + variant + ".dot"
with open(dot_file_path, 'w') as dot_file:
rdf2dot(self.gwascatalog.graph, dot_file)
# debug
LOG.debug(
"Reference graph: %s",
self.gwascatalog.graph.serialize(
format="turtle").decode("utf-8"))
reference_ttl = TTL_PATH + variant + '.ttl'
self.assertTrue(
TestUtils.test_graph_equality(reference_ttl,
self.gwascatalog.graph))
def test_parse(self):
for rcv in RCVS:
output_nt = rcv + '.nt'
input_xml = rcv + '.xml.gz'
reference_ttl = TTL_PATH + rcv + '.ttl'
with self.subTest(rcv=rcv):
mock_args = [
"test_clinvar.py", "--inputdir", XML_PATH, "--filename",
input_xml, "--mapfile", MAP_FILE, "--destination", NT_PATH,
"--output", output_nt
]
patch('sys.argv', mock_args).start()
clinvar_parse()
query_graph = RDFGraph()
query_graph.bind_all_namespaces()
query_graph.parse(NT_PATH + output_nt, format='nt')
with open(reference_ttl, 'r') as ref_fh:
ref_graph = "\n".join(ref_fh.readlines())
# debug
LOG.debug(
"Reference graph: %s",
query_graph.serialize(format="turtle").decode("utf-8"))
# Convert output from ClinVar parse to dot then png
dot_file_path = DOT_PATH + rcv + ".dot"
with open(dot_file_path, 'w') as dot_file:
rdf2dot(query_graph, dot_file)
self.assertTrue(
TestUtils.test_graph_equality(ref_graph, query_graph))
def test_parse(self):
"""
Runs WormBase.parse() and outputs dot file for each allele
This is less of a unit test and more for viewing the
output of an entire run on a single allele,
dot files can be converted to images using
scripts/dot-to-svg.sh
"""
graph_opts = {'rankdir': 'LR'}
for gene in GENES:
with self.subTest(gene_id=gene):
self.tearDownAndSetUp()
self.wormbase.rawdir = RAW_PATH + '/' + gene
self.wormbase.version_num = 'test_version'
self.wormbase.parse()
dot_file_path = DOT_PATH + gene + ".dot"
with open(dot_file_path, 'w') as dot_file:
rdf2dot(self.wormbase.graph, dot_file, graph_opts)
def test_parse(self):
"""
Runs FlyBase.parse() and outputs dot file for each allele
This is less of a unit test and more for viewing the
output of an entire run on a single allele,
dot files can be converted to images using
scripts/dot-to-svg.sh
"""
graph_opts = {
'rankdir': 'LR'
}
for allele in ALLELES:
with self.subTest(allele_id=allele):
self.tearDownAndSetUp()
self.flybase.rawdir = RAW_PATH + '/' + allele
self.flybase.parse()
dot_file_path = DOT_PATH + allele + ".dot"
with open(dot_file_path, 'w') as dot_file:
rdf2dot(self.flybase.graph, dot_file, graph_opts)
