def testReadOnlySubAlignment(self):
print("======= starting testReadOnlySubAlignment =========")
alg = MutableAlignment()
alg.read_filepath("data/mock/pyrg/sate.fasta")
subset = list(alg.keys())[9:12]
readonly_subalignment = ReadonlySubalignment(subset, alg)
print("subalignment is:\n\n", readonly_subalignment)
assert len(readonly_subalignment) == 3, len(readonly_subalignment)
assert set(readonly_subalignment.keys()) == set(
readonly_subalignment.get_sequence_names()) == set(
subset
), "Subalignment keys not matching given keys %s vs %s" % (list(
readonly_subalignment.keys()), subset)
for (k, s) in list(readonly_subalignment.items()):
assert k in subset, "%s not found in subset but returned by subalignment" % k
assert s == alg[
k], "sequence associated with %k not matching parent alignment" % k
try:
readonly_subalignment[2] = "ACGT"
assert False, "Readony alignment is successfully modified. "
except TypeError:
pass
assert readonly_subalignment.get_length() == alg.get_length(
), "alignment length should not change"
assert readonly_subalignment.is_aligned() == True
assert readonly_subalignment.is_all_gap(
2) == True, "Site 2 should be all gaps"
assert readonly_subalignment.is_all_gap(
150) == False, "Site 100 should not be all gaps"
readonly_subalignment.write_to_path("data/mock/pyrg/sate.sub.fasta")
mutable_subalignment = readonly_subalignment.get_mutable_alignment()
mutable_subalignment.delete_all_gap()
assert all([
not mutable_subalignment.is_all_gap(i)
for i in range(0, mutable_subalignment.get_length())
])
print("======= finishing testReadOnlySubAlignment =========")
def testReadOnlySubAlignment(self):
alg = MutableAlignment()
alg.read_filepath(get_data_path("mock/pyrg/sate.fasta"))
subset = [
'NC_008701_720717_722309', 'NC_013156_149033_150643',
'NC_013887_802739_801129'
]
readonly_subalignment = ReadonlySubalignment(subset, alg)
assert len(readonly_subalignment) == 3, len(readonly_subalignment)
assert set(readonly_subalignment.keys()) == set(
readonly_subalignment.get_sequence_names()) == set(subset), \
"Subalignment keys not matching given keys %s vs %s" % (
list(readonly_subalignment.keys()), subset)
for (k, s) in list(readonly_subalignment.items()):
assert k in subset, \
"%s not found in subset but returned by subalignment" % k
assert s == alg[k], \
"sequence associated with %s not matching parent alignment" % k
try:
readonly_subalignment[2] = "ACGT"
assert False, "Readony alignment is successfully modified. "
except TypeError:
pass
assert readonly_subalignment.get_length() == alg.get_length(), \
"alignment length should not change"
assert readonly_subalignment.is_aligned() is True
assert readonly_subalignment.is_all_gap(2) is True, \
"Site 2 should be all gaps"
assert readonly_subalignment.is_all_gap(150) is False, \
"Site 100 should not be all gaps"
readonly_subalignment.write_to_path(
self.fp_dummy1) # "mock/pyrg/sate.sub.fasta"
mutable_subalignment = readonly_subalignment.get_mutable_alignment()
mutable_subalignment.delete_all_gap()
assert all([
not mutable_subalignment.is_all_gap(i)
for i in range(0, mutable_subalignment.get_length())
])
def testReadOnlySubAlignment(self):
alg = MutableAlignment()
alg.read_filepath(get_data_path("mock/pyrg/sate.fasta"))
subset = ['NC_008701_720717_722309', 'NC_013156_149033_150643',
'NC_013887_802739_801129']
readonly_subalignment = ReadonlySubalignment(subset, alg)
assert len(readonly_subalignment) == 3, len(readonly_subalignment)
assert set(readonly_subalignment.keys()) == set(
readonly_subalignment.get_sequence_names()) == set(subset), \
"Subalignment keys not matching given keys %s vs %s" % (
list(readonly_subalignment.keys()), subset)
for (k, s) in list(readonly_subalignment.items()):
assert k in subset, \
"%s not found in subset but returned by subalignment" % k
assert s == alg[k], \
"sequence associated with %k not matching parent alignment" % k
try:
readonly_subalignment[2] = "ACGT"
assert False, "Readony alignment is successfully modified. "
except TypeError:
pass
assert readonly_subalignment.get_length() == alg.get_length(), \
"alignment length should not change"
assert readonly_subalignment.is_aligned() is True
assert readonly_subalignment.is_all_gap(2) is True, \
"Site 2 should be all gaps"
assert readonly_subalignment.is_all_gap(150) is False, \
"Site 100 should not be all gaps"
readonly_subalignment.write_to_path(
self.fp_dummy1) # "mock/pyrg/sate.sub.fasta"
mutable_subalignment = readonly_subalignment.get_mutable_alignment()
mutable_subalignment.delete_all_gap()
assert all([not mutable_subalignment.is_all_gap(i)
for i in range(0, mutable_subalignment.get_length())])
def testReadOnlySubAlignment(self):
print "======= starting testReadOnlySubAlignment ========="
alg = MutableAlignment()
alg.read_filepath("data/mock/pyrg/sate.fasta")
subset = alg.keys()[9:12]
readonly_subalignment = ReadonlySubalignment(subset, alg)
print "subalignment is:\n\n", readonly_subalignment
assert len(readonly_subalignment) == 3, len(readonly_subalignment)
assert readonly_subalignment.keys() == readonly_subalignment.get_sequence_names() == subset, "Subalignment keys not matching given keys %s vs %s" %(readonly_subalignment.keys() , subset)
for (k, s) in readonly_subalignment.items():
assert k in subset, "%s not found in subset but returned by subalignment" %k
assert s == alg[k], "sequence associated with %k not matching parent alignment" %k
try:
readonly_subalignment[2] = "ACGT"
assert False, "Readony alignment is successfully modified. "
except TypeError:
pass
assert readonly_subalignment.get_length() == alg.get_length(), "alignment length should not change"
assert readonly_subalignment.is_aligned() == True
assert readonly_subalignment.is_all_gap(2) == True, "Site 2 should be all gaps"
assert readonly_subalignment.is_all_gap(150) == False, "Site 100 should not be all gaps"
readonly_subalignment.write_to_path("data/mock/pyrg/sate.sub.fasta")
mutable_subalignment = readonly_subalignment.get_mutable_alignment()
mutable_subalignment.delete_all_gap()
assert all([not mutable_subalignment.is_all_gap(i) for i in xrange(0,mutable_subalignment.get_length())])
print "======= finishing testReadOnlySubAlignment ========="