def testExtendedAlignment(self):
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(get_data_path("simulated/test.fasta"))
alg.delete_all_gap()
tlen = alg.get_length()
frg = MutableAlignment()
frg.read_filepath(get_data_path("simulated/test.fas"))
# print frg.get_num_taxa()
pp = SeppProblem(list(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 list(frg.keys()) if int(k[-1]) >= 9], frg)
cp2.fragments = ReadonlySubalignment(
[k for k in list(frg.keys()) if int(k[-1]) <= 1], frg)
cp1labels = cp1.write_subalignment_without_allgap_columns(
self.fp_dummy1) # tmp/cp1.fasta
cp2labels = cp2.write_subalignment_without_allgap_columns(
self.fp_dummy2) # tmp/cp2.fasta
tmp = MutableAlignment().read_filepath(self.fp_dummy1)
assert all(
[not tmp.is_all_gap(pos) for pos in range(0, tmp.get_length())])
tmp = MutableAlignment().read_filepath(self.fp_dummy2)
assert all(
[not tmp.is_all_gap(pos) for pos in range(0, tmp.get_length())])
cp1.fragments.write_to_path(self.fp_dummy3) # tmp/cp1.frags.fas
cp2.fragments.write_to_path(self.fp_dummy4) # 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(self.fp_dummy1,
get_data_path("tmp/cp1.extended.sto"))
ext1.relabel_original_columns(cp1labels)
ext2 = ExtendedAlignment(cp2.fragments)
ext2.build_extended_alignment(self.fp_dummy2,
get_data_path("tmp/cp2.extended.sto"))
ext2.relabel_original_columns(cp2labels)
extmerger = ExtendedAlignment([])
extmerger.merge_in(ext1)
mixed = extmerger.merge_in(ext2)
extmerger.write_to_path(self.fp_dummy5) # 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])
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(extmerger.get_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 list(tmp.items())]), \
"merged alignment should match original alignment"
def testExtendedAlignment(self):
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(get_data_path("simulated/test.fasta"))
alg.delete_all_gap()
tlen = alg.get_length()
frg = MutableAlignment()
frg.read_filepath(get_data_path("simulated/test.fas"))
# print frg.get_num_taxa()
pp = SeppProblem(list(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 list(frg.keys()) if int(k[-1]) >= 9], frg)
cp2.fragments = ReadonlySubalignment(
[k for k in list(frg.keys()) if int(k[-1]) <= 1], frg)
cp1labels = cp1.write_subalignment_without_allgap_columns(
self.fp_dummy1) # tmp/cp1.fasta
cp2labels = cp2.write_subalignment_without_allgap_columns(
self.fp_dummy2) # tmp/cp2.fasta
tmp = MutableAlignment().read_filepath(self.fp_dummy1)
assert all([not tmp.is_all_gap(pos)
for pos in range(0, tmp.get_length())])
tmp = MutableAlignment().read_filepath(self.fp_dummy2)
assert all([not tmp.is_all_gap(pos)
for pos in range(0, tmp.get_length())])
cp1.fragments.write_to_path(self.fp_dummy3) # tmp/cp1.frags.fas
cp2.fragments.write_to_path(self.fp_dummy4) # 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(
self.fp_dummy1,
get_data_path("tmp/cp1.extended.sto"))
ext1.relabel_original_columns(cp1labels)
ext2 = ExtendedAlignment(cp2.fragments)
ext2.build_extended_alignment(
self.fp_dummy2,
get_data_path("tmp/cp2.extended.sto"))
ext2.relabel_original_columns(cp2labels)
extmerger = ExtendedAlignment([])
extmerger.merge_in(ext1)
mixed = extmerger.merge_in(ext2)
extmerger.write_to_path(self.fp_dummy5) # 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])
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(extmerger.get_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 list(tmp.items())]), \
"merged alignment should match original alignment"
