def get_subalignment(self):
'''
If subalignment is not set before, automatically builds a readonly
subalignment for this subproblem, based on the taxa assigned to this subproblem.
Otherwise, returns the saves subalignment.
'''
if self.__subalignment == None:
if isinstance(self.parent, SeppProblem) or hasattr(
self.parent, "subalignment"):
self.__subalignment = ReadonlySubalignment(
self.taxa, self.parent.subalignment)
#print sorted(self.__subalignment.keys())
#print sorted(self.parent.subalignment.keys())
#print "..... %s %s" %(self.label, self.parent.label)
else:
raise TypeError(
"parent object %s has no subalignment attribute" %
self.parent)
return self.__subalignment
def testExtendedAlignment(self):
print "======= starting testExtendedAlignment ========="
subset = [
"SFIF", "SFII", "SCFC", "SGHD", "SDCC", "SBGE", "SFBB", "SDI",
"SCGB", "SJGF", "SGBI", "SCJA", "SGAD", "SHEB", "SFHB", "SDJI",
"SHED", "SJJJ", "SBBE", "SCCH", "SDJB", "SDAC", "SHEH", "SFDC",
"SFEI", "SHHB", "SC", "SIAB", "SDDI", "SBCB", "SJB", "SEBD",
"SFGD", "SHA", "SIDA", "SGHI", "SGIB", "SBFJ", "SFIE", "SCJF",
"SJHJ", "SJBG", "SEJI", "SFFF", "SJ", "SIII", "SJHH", "SEIH",
"SBDC", "SHDJ", "SJDD", "SGDB", "SIHA", "SIBB", "SECC", "SCAD",
"SGBB", "SGIF", "SJHC", "SFCD", "SEAA", "SEFF", "SDFG", "SDJE",
"SCFG", "SFH", "SCJ", "SDDD", "SEGD", "SCIH", "SDAG", "SCJE",
"SFAJ", "SIDJ", "SE", "SHBC", "SJFF", "SCHD", "SBHA", "SEDF",
"SFAF", "SEDD", "SDHD", "SGJD", "SIBH", "SGDF", "SIFA", "SJGA",
"SIJB", "SFI", "SGA", "SBFC", "SBJA", "SFFC", "SFDH", "SFEE",
"SBDF", "SGBJ", "SDHE", "SJIB", "SHHI", "SIDE", "SJII"
]
alg = MutableAlignment()
alg.read_filepath("data/simulated/test.fasta")
alg.delete_all_gap()
tlen = alg.get_length()
frg = MutableAlignment()
frg.read_filepath("data/simulated/test.fas")
#print frg.get_num_taxa()
pp = SeppProblem(alg.keys())
pp.fragments = frg
pp.subalignment = alg
cp1 = SeppProblem(subset, pp)
cp2 = SeppProblem(list(set(alg.keys()) - set(subset)), pp)
cp1.fragments = ReadonlySubalignment(
[k for k in frg.keys() if int(k[-1]) >= 9], frg)
cp2.fragments = ReadonlySubalignment(
[k for k in frg.keys() if int(k[-1]) <= 1], frg)
cp1labels = cp1.write_subalignment_without_allgap_columns(
"data/tmp/cp1.fasta")
cp2labels = cp2.write_subalignment_without_allgap_columns(
"data/tmp/cp2.fasta")
tmp = MutableAlignment().read_filepath("data/tmp/cp1.fasta")
assert all(
[not tmp.is_all_gap(pos) for pos in xrange(0, tmp.get_length())])
tmp = MutableAlignment().read_filepath("data/tmp/cp2.fasta")
assert all(
[not tmp.is_all_gap(pos) for pos in xrange(0, tmp.get_length())])
cp1.fragments.write_to_path("data/tmp/cp1.frags.fas")
cp2.fragments.write_to_path("data/tmp/cp2.frags.fas")
'''We have done the hmmalign before. don't worry about that right now'''
ext1 = ExtendedAlignment(cp1.fragments)
ext1.build_extended_alignment("data/tmp/cp1.fasta",
"data/tmp/cp1.extended.sto")
ext1.relabel_original_columns(cp1labels)
ext2 = ExtendedAlignment(cp2.fragments)
ext2.build_extended_alignment("data/tmp/cp2.fasta",
"data/tmp/cp2.extended.sto")
ext2.relabel_original_columns(cp2labels)
extmerger = ExtendedAlignment([])
extmerger.merge_in(ext1)
mixed = extmerger.merge_in(ext2)
extmerger.write_to_path("data/tmp/extended.merged.fasta")
assert extmerger.is_aligned(), "Merged alignment is not aligned"
in1 = len([x for x in ext1._col_labels if x < 0])
in2 = len([x for x in ext2._col_labels if x < 0])
print "Merged:%d. Insertion1:%d Insertion2:%d BaseLen:%d" % (
extmerger.get_length(), in1, in2, tlen)
assert (in1 + in2 + tlen - mixed) == extmerger.get_length(
), "Lengths don't match up after merging. Merged:%d. Insertion1:%d Insertion2:%d BaseLen:%d Mixed-insertion: %d" % (
extmerger.get_length(), in1, in2, tlen, mixed)
assert (in1 + in2 - mixed) == len(
list(extmerger.iter_insertion_columns())
), "Columns are not correctly labeled after merging. Merged insertion count:%d. Insertion1:%d Insertion2:%d Mixed-insertion: %d" % (
len(list(extmerger.iter_insertion_columns())), in1, in1, mixed)
tmp = extmerger.get_base_readonly_alignment().get_mutable_alignment()
tmp.delete_all_gap()
assert tmp.is_aligned(), "merged alignment should be aligned!"
assert tmp.get_length() == tlen, "merged alignment has wrong length"
assert all([alg[k] == s for (k, s) in tmp.items()
]), "merged alignment should match original alignment"
print "======= finished testExtendedAlignment ========="
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 ========="
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 ========="
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())])