def __str__(self) :
out = StringIO()
print('## LogoData', file=out)
print('# First column is position number, counting from zero', file=out)
print('# Subsequent columns are raw symbol counts', file=out)
print('# Entropy is mean entropy measured in nats.' , file=out)
print('# Low and High are the 95% confidence limits.', file=out)
print('# Weight is the fraction of non-gap symbols in the column.', file=out)
print('#\t', file=out)
# Show column names
print('#', end='\t', file=out)
for a in self.alphabet :
print(a, end=' \t', file=out)
print('Entropy\tLow\tHigh\tWeight', file=out)
# Write the data table
for i in range(self.length) :
print(i + 1, end=' \t', file=out)
for c in self.counts[i]:
print(c, end=' \t', file=out)
print("%6.4f" % self.entropy[i], end=' \t', file=out)
if self.entropy_interval is not None:
print("%6.4f" % self.entropy_interval[i][0], end=' \t',
file=out)
print("%6.4f" % self.entropy_interval[i][1], end=' \t',
file=out)
else :
print('\t', '\t', end='', file=out)
if self.weight is not None :
print("%6.4f" % self.weight[i], end='', file=out)
print('', file=out)
print('# End LogoData', file=out)
return out.getvalue()
def testParse(self):
f = testdata_stream('scop/dir.cla.scop.txt_test')
try:
cla = f.read()
f.close()
f = testdata_stream('scop/dir.des.scop.txt_test')
des = f.read()
f.close()
f = testdata_stream('scop/dir.hie.scop.txt_test')
hie = f.read()
finally:
f.close()
scop = Scop.parse_files(StringIO(cla), StringIO(des), StringIO(hie))
cla_out = StringIO()
scop.write_cla(cla_out)
assert cla_out.getvalue() == cla, cla_out.getvalue()
des_out = StringIO()
scop.write_des(des_out)
assert des_out.getvalue() == des, des_out.getvalue()
hie_out = StringIO()
scop.write_hie(hie_out)
assert hie_out.getvalue() == hie, hie_out.getvalue()
domain = scop.domains_by_sid["d1hbia_"]
self.assertEqual(domain.sunid, 14996)
domains = scop.domains
self.assertEqual(len(domains), 14)
self.assertEqual(domains[4].sunid, 14988)
self.assertFalse(-111 in scop.nodes_by_sunid)
self.assertFalse("no such domain" in scop.domains_by_sid)
def testParse(self):
f = testdata_stream('scop/dir.cla.scop.txt_test')
try:
cla = f.read()
f.close()
f = testdata_stream('scop/dir.des.scop.txt_test')
des = f.read()
f.close()
f = testdata_stream('scop/dir.hie.scop.txt_test')
hie = f.read()
finally:
f.close()
scop = Scop.parse_files(StringIO(cla), StringIO(des), StringIO(hie))
cla_out = StringIO()
scop.write_cla(cla_out)
assert cla_out.getvalue() == cla, cla_out.getvalue()
des_out = StringIO()
scop.write_des(des_out)
assert des_out.getvalue() == des, des_out.getvalue()
hie_out = StringIO()
scop.write_hie(hie_out)
assert hie_out.getvalue() == hie, hie_out.getvalue()
domain = scop.domains_by_sid["d1hbia_"]
self.assertEqual(domain.sunid, 14996)
domains = scop.domains
self.assertEqual(len(domains), 14)
self.assertEqual(domains[4].sunid, 14988)
self.assertFalse(-111 in scop.nodes_by_sunid)
self.assertFalse("no such domain" in scop.domains_by_sid )
