def test_to_json(self):
"""test the json serialization method"""
expected_json = """{"refseqs": ["NM_013464", "NM_001621"], "sourcefile": "5", "pssm": [[0.1000, 0.3000, 0.4000, 0.2000], [0.5000, 0.1000, 0.1000, 0.3000], [0.2000, 0.4000, 0.3000, 0.1000]], "antisense": "True", "dbd": "5", "numseqs": "5", "species": null, "symbols": ["Runx3", "Ahr"], "source": "5", "seqpos_results": {"numhits": null, "zscore": null, "pvalue": null, "meanposition": null, "cutoff": null}, "entrezs": ["25690", "11622", "196"], "fullname": "5", "pmid": "5", "id": "5"}"""
dom = parse('fixtures/goodMotif.xml')
#print dom.documentElement.tagName
foo = Motif.from_xml(dom.documentElement)
#print foo.to_json()
self.assertEqual(foo.to_json(), expected_json)
def test_from_xml_optional_attr(self):
"""Test that a motif with none of the optional attributes is read in correctly"""
pssm = [[0.1, 0.3, 0.4, 0.2], [0.5, 0.1, 0.1, 0.3],
[0.2, 0.4, 0.3, 0.1]]
foo = Motif()
foo.id = "5"
dom = parse('fixtures/goodMotifOpt.xml')
#print dom.documentElement.tagName
bar = Motif.from_xml(dom.documentElement)
#print bar
self.assertTrue(foo.equals(bar))
def test_from_xml(self):
"""test the xml motif parser; goodMotif.xml should equal foo"""
pssm = [[0.1, 0.3, 0.4, 0.2], [0.5, 0.1, 0.1, 0.3],
[0.2, 0.4, 0.3, 0.1]]
foo = Motif()
for attr in AcceptanceTests._ATTRIBUTES:
setattr(foo, attr, '5')
foo.id = "5"
foo.symbols = ["Runx3", "Ahr"]
foo.entrezs = ["25690", "11622", "196"]
foo.refseqs = ["NM_013464", "NM_001621"]
foo.antisense = True
foo.setpssm(pssm)
#print foo
dom = parse('fixtures/goodMotif.xml')
#print dom.documentElement.tagName
bar = Motif.from_xml(dom.documentElement)
#print bar
self.assertTrue(foo.equals(bar))
def test_from_xml2(self):
"""test the xml motif parser w/o reading from file--use to_xml"""
pssm = [[0.1, 0.3, 0.4, 0.2], [0.5, 0.1, 0.1, 0.3],
[0.2, 0.4, 0.3, 0.1]]
foo = Motif()
foo.id = "19"
foo.symbols = ["Runx3", "Ahr"]
foo.entrezs = ["25690", "11622", "196"]
foo.refseqs = ["NM_013464", "NM_001621"]
foo.antisense = True
foo.setpssm(pssm)
#print foo
fuz = foo.to_xml()
#print fuz
dom = parseString(fuz)
bar = Motif.from_xml(dom.documentElement)
#print bar
#print "%s, %s" % (foo.id, bar.id)
#print foo.id == bar.id
self.assertTrue(foo.equals(bar))