def testParse(self):
f = open("./SCOP/dir.cla.scop.txt_test")
try:
cla = f.read()
f.close()
f = open("./SCOP/dir.des.scop.txt_test")
des = f.read()
f.close()
f = open("./SCOP/dir.hie.scop.txt_test")
hie = f.read()
finally:
f.close()
scop = Scop(StringIO(cla), StringIO(des), StringIO(hie))
cla_out = StringIO()
scop.write_cla(cla_out)
lines = zip(cla.rstrip().split('\n'),
cla_out.getvalue().rstrip().split('\n'))
for expected_line, line in lines:
self.assertTrue(self._compare_cla_lines(expected_line, line))
des_out = StringIO()
scop.write_des(des_out)
self.assertEqual(des_out.getvalue(), des)
hie_out = StringIO()
scop.write_hie(hie_out)
self.assertEqual(hie_out.getvalue(), hie)
domain = scop.getDomainBySid("d1hbia_")
self.assertEqual(domain.sunid, 14996)
domains = scop.getDomains()
self.assertEqual(len(domains), 14)
self.assertEqual(domains[4].sunid, 14988)
dom = scop.getNodeBySunid(-111)
self.assertEqual(dom, None)
dom = scop.getDomainBySid("no such domain")
self.assertEqual(dom, None)
def testParse(self):
f = open("./SCOP/dir.cla.scop.txt_test")
try:
cla = f.read()
f.close()
f = open("./SCOP/dir.des.scop.txt_test")
des = f.read()
f.close()
f = open("./SCOP/dir.hie.scop.txt_test")
hie = f.read()
finally:
f.close()
scop = Scop(StringIO(cla), StringIO(des), StringIO(hie))
cla_out = StringIO()
scop.write_cla(cla_out)
lines = zip(cla.rstrip().split("\n"),
cla_out.getvalue().rstrip().split("\n"))
for expected_line, line in lines:
self.assertTrue(self._compare_cla_lines(expected_line, line))
des_out = StringIO()
scop.write_des(des_out)
self.assertEqual(des_out.getvalue(), des)
hie_out = StringIO()
scop.write_hie(hie_out)
self.assertEqual(hie_out.getvalue(), hie)
domain = scop.getDomainBySid("d1hbia_")
self.assertEqual(domain.sunid, 14996)
domains = scop.getDomains()
self.assertEqual(len(domains), 14)
self.assertEqual(domains[4].sunid, 14988)
dom = scop.getNodeBySunid(-111)
self.assertEqual(dom, None)
dom = scop.getDomainBySid("no such domain")
self.assertEqual(dom, None)
def testGetAscendent(self):
scop = Scop(dir_path="SCOP", version="test")
domain = scop.getDomainBySid("d1hbia_")
# get the fold
fold = domain.getAscendent("cf")
self.assertEqual(fold.sunid, 46457)
# get the superfamily
sf = domain.getAscendent("superfamily")
self.assertEqual(sf.sunid, 46458)
# px has no px ascendent
px = domain.getAscendent("px")
self.assertEqual(px, None)
# an sf has no px ascendent
px2 = sf.getAscendent("px")
self.assertEqual(px2, None)
def testGetAscendent(self):
scop = Scop(dir_path="SCOP", version="test")
domain = scop.getDomainBySid("d1hbia_")
# get the fold
fold = domain.getAscendent('cf')
self.assertEqual(fold.sunid, 46457)
# get the superfamily
sf = domain.getAscendent('superfamily')
self.assertEqual(sf.sunid, 46458)
# px has no px ascendent
px = domain.getAscendent('px')
self.assertEqual(px, None)
# an sf has no px ascendent
px2 = sf.getAscendent('px')
self.assertEqual(px2, None)
class AstralTests(unittest.TestCase):
def setUp(self):
self.scop = Scop(dir_path="SCOP", version="test")
self.astral = Astral(scop=self.scop, dir_path="SCOP", version="test")
def testGetSeq(self):
self.assertEqual(str(self.astral.getSeqBySid("d3sdha_")), "AAAAA")
self.assertEqual(str(self.astral.getSeqBySid("d4hbib_")), "KKKKK")
dom = self.scop.getDomainBySid("d3sdha_")
self.assertEqual(str(self.astral.getSeq(dom)), "AAAAA")
def testConstructWithCustomFile(self):
scop = Scop(dir_path="SCOP", version="test")
astral = Astral(
scop=scop,
astral_file="SCOP/scopseq-test/astral-scopdom-seqres-all-test.fa")
self.assertEqual(str(astral.getSeqBySid("d3sdha_")), "AAAAA")
self.assertEqual(str(astral.getSeqBySid("d4hbib_")), "KKKKK")
def testGetDomainsFromFile(self):
filename = "SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-20-test.id"
domains = self.astral.getAstralDomainsFromFile(filename)
self.assertEqual(len(domains), 3)
self.assertEqual(domains[0].sid, "d3sdha_")
self.assertEqual(domains[1].sid, "d4hbib_")
self.assertEqual(domains[2].sid, "d5hbia_")
def testGetDomainsClustered(self):
domains1 = self.astral.domainsClusteredById(20)
self.assertEqual(len(domains1), 3)
self.assertEqual(domains1[0].sid, "d3sdha_")
self.assertEqual(domains1[1].sid, "d4hbib_")
self.assertEqual(domains1[2].sid, "d5hbia_")
domains2 = self.astral.domainsClusteredByEv(1e-15)
self.assertEqual(len(domains2), 1)
class AstralTests(unittest.TestCase):
def setUp(self):
self.scop = Scop(dir_path="SCOP", version="test")
self.astral = Astral(scop=self.scop, dir_path="SCOP", version="test")
def testGetSeq(self):
self.assertEqual(str(self.astral.getSeqBySid('d3sdha_')), "AAAAA")
self.assertEqual(str(self.astral.getSeqBySid('d4hbib_')), "KKKKK")
dom = self.scop.getDomainBySid('d3sdha_')
self.assertEqual(str(self.astral.getSeq(dom)), "AAAAA")
def testConstructWithCustomFile(self):
scop = Scop(dir_path="SCOP", version="test")
astral = Astral(scop=scop,
astral_file="SCOP/scopseq-test/astral-scopdom-seqres-all-test.fa")
self.assertEqual(str(astral.getSeqBySid('d3sdha_')), "AAAAA")
self.assertEqual(str(astral.getSeqBySid('d4hbib_')), "KKKKK")
def testGetDomainsFromFile(self):
filename = "SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-20-test.id"
domains = self.astral.getAstralDomainsFromFile(filename)
self.assertEqual(len(domains), 3)
self.assertEqual(domains[0].sid, "d3sdha_")
self.assertEqual(domains[1].sid, "d4hbib_")
self.assertEqual(domains[2].sid, "d5hbia_")
def testGetDomainsClustered(self):
domains1 = self.astral.domainsClusteredById(20)
self.assertEqual(len(domains1), 3)
self.assertEqual(domains1[0].sid, "d3sdha_")
self.assertEqual(domains1[1].sid, "d4hbib_")
self.assertEqual(domains1[2].sid, "d5hbia_")
domains2 = self.astral.domainsClusteredByEv(1e-15)
self.assertEqual(len(domains2), 1)
def testConstructFromDirectory(self):
scop = Scop(dir_path="SCOP", version="test")
self.assertTrue(isinstance(scop, Scop))
domain = scop.getDomainBySid("d1hbia_")
self.assertEqual(domain.sunid, 14996)
def testConstructFromDirectory(self):
scop = Scop(dir_path="SCOP", version="test")
self.assertTrue(isinstance(scop, Scop))
domain = scop.getDomainBySid("d1hbia_")
self.assertEqual(domain.sunid, 14996)
samples = np.array([v for i, v in enumerate(scop40) if i in fold1[1]])
# sf_sunid of scop100 (sid)
px = np.array([x.sid for x in scop100_hie.getNodeBySunid(sf_sunid).getDescendents('px')])
# select only sf_sunid in scop40 from scop100
isect = np.intersect1d(samples, px)
# select half of sf_sunid only in scop40 for test data
fold1 = next(KFold(n_splits=test_n_splits, shuffle=True).split(isect))
tests = np.array([v for i, v in enumerate(isect) if i in fold1[1]])
np.save(Path(f'data/test/scop40_{n_splits}fold_sf{sf_sunid}_testdata_{test_n_splits}fold.npy'), tests)
# select domain sids only in scop40 for training data
train = np.setdiff1d(samples, tests)
np.save(Path(f'data/train/scop40_{n_splits}fold_trainingdata.npy'), train)
# {sf: [sid]} list for making alignment pairs in the same superfamily
hie = {}
for i in train:
dom = scop100_hie.getDomainBySid(i)
if dom:
sf = dom.getAscendent('sf').sccs
else:
# FIX: Why nothing?
continue
if sf in hie:
hie[sf].append(i)
else:
hie[sf] = [i]
pickle.dump(hie, Path(f'data/train/scop40_{n_splits}fold_sf{sf_sunid}_hie.pkl').open('wb'))
else:
train = np.array([x for x in scop40 if x not in test_data])
np.save(Path(f'data/train/scop40_{n_splits}fold.npy'), train)
test = np.array(test_data)
np.save(Path(f'data/test/scop40_{n_splits}fold.npy'), test)
