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_convenience_fns(self):
"""Make convenience fns like getpvalue, etc. work"""
foo = Motif()
for attr in AcceptanceTests._results_fields:
#COULD have done this instead to be explicit, but my way is cleaner
#self.assertEqual(getattr(foo, "get"+attr).__call__(), None)
self.assertEqual(getattr(foo, "get" + attr)(), None)
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_equals(self):
"""Tests the motif.equals fn"""
foo = Motif()
bar = Motif()
foo.id = 'M00134'
bar.id = 'M00134'
self.assertTrue(foo.equals(bar))
self.assertTrue(foo.equals(foo))
def test_to_xml(self):
"""test the xml serialization method"""
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.symbols = ["Runx3", "Ahr"]
foo.entrezs = ["25690", "11622", "196"]
foo.refseqs = ["NM_013464", "NM_001621"]
foo.antisense = True
foo.setpssm(pssm)
xml_str = foo.to_xml(print_non_schema=True)
dom = parseString(xml_str)
#verify the output
#PUNT--i'm not up for it right now
self.assertTrue(True)
def test_seqpos(self):
class Bar:
pass
pssm = [[0.49, 0.167, 0.01, 0.333], [0.924, 0.01, 0.056, 0.01],
[0.924, 0.01, 0.056, 0.01], [0.01, 0.97, 0.01, 0.01],
[0.01, 0.97, 0.01, 0.01], [0.313, 0.01, 0.667, 0.01],
[0.01, 0.97, 0.01, 0.01], [0.97, 0.01, 0.01, 0.01],
[0.591, 0.01, 0.389, 0.01]]
#read in an actual chip regions sequence
f = open("fixtures/chipRegionSeq.txt")
seq = eval(f.readline())
#print seq
f.close()
chip_regions = Bar()
chip_regions.sequence = seq
chip_regions.preprocessed_regions = True
foo = Motif()
foo.setpssm(pssm)
foo.seqpos(chip_regions)
#print foo
seqpos_results_ref =\
{'cutoff': 4.9475970072872455, 'zscore': -8.547918739697856,
'pssm': [[0.50764525993883791, 0.17125382262996941, 0.027522935779816515, 0.29357798165137616],
[0.80122324159021407, 0.033639143730886847, 0.1529051987767584, 0.012232415902140673],
[0.86850152905198774, 0.015290519877675841, 0.10703363914373089, 0.0091743119266055051],
[0.015290519877675841, 0.95718654434250761, 0.0091743119266055051, 0.01834862385321101],
[0.01834862385321101, 0.94189602446483178, 0.01834862385321101, 0.021406727828746176],
[0.61467889908256879, 0.030581039755351681, 0.31804281345565749, 0.03669724770642202],
[0.01834862385321101, 0.94495412844036697, 0.027522935779816515, 0.0091743119266055051],
[0.90825688073394495, 0.024464831804281346, 0.03669724770642202, 0.030581039755351681],
[0.47094801223241589, 0.055045871559633031, 0.44954128440366975, 0.024464831804281346]],
'meanposition': -0.14154048514881779, 'numhits': 255,
'pvalue': 6.2663951031948087e-18}
list = ['cutoff', 'zscore', 'meanposition', 'numhits', 'pvalue']
for attr in list:
self.assertTrue(
feq(foo.seqpos_results[attr], seqpos_results_ref[attr]))
#compare pssms
for r in range(len(seqpos_results_ref['pssm'])):
for c in range(len(seqpos_results_ref['pssm'][0])):
self.assertTrue(
feq(seqpos_results_ref['pssm'][r][c],
foo.seqpos_results['pssm'][r][c]))
def test_from_flat_file2(self):
"""fixtures/goodPssmObCb.txt should be a valid motif"""
foo = Motif.from_flat_file('fixtures/goodPssmObCb.txt')
self.assertTrue(Motif._validpssm(foo.pssm))
def test_not_equals(self):
"""Tests the motif.equals fn"""
foo = Motif()
bar = Motif()
foo.id = 'M00134'
self.assertFalse(foo.equals(bar))
def test_validpssm(self):
"""This is a valid pssm, it should pass"""
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]]
self.assertTrue(Motif._validpssm(pssm))
def test_seqpos_results_set_to_none(self):
"""Make sure that seqpos_results dictionary is set to None"""
foo = Motif()
for attr in AcceptanceTests._results_fields:
self.assertEqual(foo.seqpos_results[attr], None)
def test_attributes_set_to_none(self):
"""Make sure that all of the attributes are all initialized to None"""
foo = Motif()
for attr in AcceptanceTests._ATTRIBUTES:
if attr != 'seqpos_results':
self.assertEqual(getattr(foo, attr), None)
def test_seqpos_stat(self):
"""Testing the seqpos stat method:
actual data from running: MDSeqPos.py runx_small.bed mm8 -m y1h.xml
"""
pssm = [[0.49, 0.167, 0.01, 0.333], [0.924, 0.01, 0.056, 0.01],
[0.924, 0.01, 0.056, 0.01], [0.01, 0.97, 0.01, 0.01],
[0.01, 0.97, 0.01, 0.01], [0.313, 0.01, 0.667, 0.01],
[0.01, 0.97, 0.01, 0.01], [0.97, 0.01, 0.01, 0.01],
[0.591, 0.01, 0.389, 0.01]]
start = [
114, 596, 329, 208, 507, 340, 467, 239, 458, 283, 559, 281, 175,
301, 397, 623, 240, 54, 212, 511, 285, 380, 511, 116
]
end = [
123, 605, 338, 217, 516, 349, 476, 248, 467, 292, 568, 290, 184,
310, 406, 632, 249, 63, 221, 520, 294, 389, 520, 125
]
score = [
4.91170692, 5.87872267, 6.32827187, 4.73049879, 4.61262989,
6.83801079, 1.78081846, 4.05301714, 4.85997772, 2.98214078,
4.32487345, 2.78596187, 4.73322868, 5.85379267, 5.10804605,
4.35964298, 3.89328027, 7.50640059, 5.79009295, 2.93482327,
7.54800034, 3.64937592, 3.9898386, 2.86741686
]
#fracpos is an intermediate step- its here just to compare the output
frac = [
0.64430577, 0.85959438, 0.02652106, 0.35101404, 0.58190328,
0.06084243, 0.45709828, 0.25429017, 0.42901716, 0.11700468,
0.74414977, 0.12324493, 0.45397816, 0.06084243, 0.23868955,
0.94383775, 0.25117005, 0.83151326, 0.33853354, 0.59438378,
0.11076443, 0.18564743, 0.59438378, 0.63806552
]
length = 650
foo = Motif()
foo.setpssm(pssm)
foo.seqpos_stat(start, end, score, length)
self.assertEqual(foo.getnumhits(), 23)
self.assertTrue(feq(foo.getzscore(), -0.16397254440660525))
self.assertTrue(feq(foo.getpvalue(), 0.43487637881039054))
self.assertTrue(feq(foo.getmeanposition(), -0.069965407311944727))
self.assertTrue(feq(foo.getcutoff(), 1.7808184600000001))
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))
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_append(self):
ml = MotifList()
self.assertEqual(len(ml), 0)
ml.append(Motif())
self.assertEqual(len(ml), 1)
def test_no_duplicates(self):
tmp = Motif()
ml = MotifList()
ml.append(tmp)
#adding it again MUST raise DuplicateMotif Exception
self.assertRaises(DuplicateMotif, ml.append, tmp)