def test_wl2qlc(self):
stamp = 'test-stamp'
out = self.tmp_path('test')
wl2qlc(self.wordlist.header, self.wordlist._data,
filename=out.as_posix(), stamp=stamp)
out = self.tmp_path('test.qlc')
with out.open(encoding='utf8') as fp:
self.assertTrue(fp.read().endswith(stamp))
# load a worldist with alignments and otuput it as string with msapairs
tmp = Alignments(test_data('good_file.tsv'), ref='cogid')
tmp.align(ref="cogid")
wl2qlc(tmp.header, tmp._data, meta=tmp._meta, filename=out.as_posix(),
stamp='stampo', ignore=[])
tmp.get_consensus(ref="cogid")
wl2qlc([h.upper()
for h in sorted(tmp.header, key=lambda x: tmp.header[x])],
tmp._data, meta=tmp._meta, filename=out.as_posix(),
stamp='stampo', ignore=[], formatter="doculect,concept")
wl2qlc([h.upper()
for h in sorted(tmp.header, key=lambda x: tmp.header[x])],
tmp._data, meta=tmp._meta, filename=out.as_posix(),
stamp='stampo', ignore=[], formatter="doculect")
def test_wl2qlc(self):
stamp = 'test-stamp'
out = self.tmp_path('test')
wl2qlc(self.wordlist.header,
self.wordlist._data,
filename=out.as_posix(),
stamp=stamp)
out = self.tmp_path('test.qlc')
with out.open(encoding='utf8') as fp:
self.assertTrue(fp.read().endswith(stamp))
# load a worldist with alignments and otuput it as string with msapairs
tmp = Alignments(test_data('good_file.tsv'), ref='cogid')
tmp.align(ref="cogid")
wl2qlc(tmp.header,
tmp._data,
meta=tmp._meta,
filename=out.as_posix(),
stamp='stampo',
ignore=[])
tmp.get_consensus(ref="cogid")
wl2qlc([
h.upper() for h in sorted(tmp.header, key=lambda x: tmp.header[x])
],
tmp._data,
meta=tmp._meta,
filename=out.as_posix(),
stamp='stampo',
ignore=[],
formatter="doculect,concept")
wl2qlc([
h.upper() for h in sorted(tmp.header, key=lambda x: tmp.header[x])
],
tmp._data,
meta=tmp._meta,
filename=out.as_posix(),
stamp='stampo',
ignore=[],
formatter="doculect")
def test_wl2qlc(tmppath, test_data, wordlist):
stamp = 'test-stamp'
out = tmppath / 'test'
wl2qlc(wordlist.header, wordlist._data, filename=str(out), stamp=stamp)
out = tmppath / 'test.qlc'
assert out.read_text(encoding='utf8').endswith(stamp)
# load a worldist with alignments and otuput it as string with msapairs
tmp = Alignments(str(test_data / 'good_file.tsv'), ref='cogid')
tmp.align(ref="cogid")
wl2qlc(tmp.header,
tmp._data,
meta=tmp._meta,
filename=str(out),
stamp='stampo',
ignore=[])
tmp.get_consensus(ref="cogid")
wl2qlc(
[h.upper() for h in sorted(tmp.header, key=lambda x: tmp.header[x])],
tmp._data,
meta=tmp._meta,
filename=out.as_posix(),
stamp='stampo',
ignore=[],
formatter="doculect,concept")
wl2qlc(
[h.upper() for h in sorted(tmp.header, key=lambda x: tmp.header[x])],
tmp._data,
meta=tmp._meta,
filename=out.as_posix(),
stamp='stampo',
ignore=[],
formatter="doculect")
def setUp(self):
WithTempDir.setUp(self)
self.alm = Alignments(test_data('KSL2.qlc'),
loans=False,
_interactive=False)
self.alm.align()
class TestAlignments(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.alm = Alignments(test_data('KSL2.qlc'),
loans=False,
_interactive=False)
self.alm.align()
def test_ipa2tokens(self):
# iterate over the keys
for key in self.alm: #.get_list(language="Turkish",flat=True):
ipa = self.alm[key, 'ipa']
tokensA = self.alm[key, 'tokensa'].split(' ')
tokensB = self.alm[key, 'tokensb'].split(' ')
new_tokensA = lp.ipa2tokens(ipa,
merge_vowels=True,
merge_geminates=False)
new_tokensB = lp.ipa2tokens(ipa,
merge_vowels=False,
merge_geminates=False)
assert tokensA == new_tokensA
assert tokensB == new_tokensB
def test_align(self):
self.alm.add_entries('cugid', self.alm._ref, lambda x: text_type(x))
self.alm.add_alignments(ref="cugid")
# align all sequences using standard params
self.alm.align(ref="cugid", alignment="alignment2")
assert self.alm.msa["cugid"]["1"]["ID"] == self.alm.msa["cogid"][1][
"ID"]
# iterate and align using the multiple function
for key, value in self.alm.msa['cogid'].items():
# first compare simple alignments
msaA = lp.SCA(value)
msaB = lp.Multiple(value['seqs'])
msaB.prog_align()
assert msaA == msaB
# now compare with different flag
msaA = lp.Multiple(
[self.alm[idx, 'tokensb'] for idx in value['ID']])
msaB = lp.Multiple([''.join(s) for s in value['seqs']],
merge_vowels=False)
msaA.lib_align()
msaB.lib_align()
assert msaA == msaB
def test_get_consensus(self):
# align all sequences using standard params
self.alm.get_consensus(consensus="consensus", classes=True)
self.alm.get_consensus(consensus="consensus")
# check whether Turkish strings are identical
self.assertEqual(
self.alm.get_list(language="Turkish", entry="consensus",
flat=True),
[
''.join(x) for x in self.alm.get_list(
language="Turkish", entry="tokens", flat=True)
])
def test_get_confidence(self):
lex = LexStat(test_data('KSL3.qlc'))
tmpDict = dict([(k, lex[k, 'numbers']) for k in lex])
self.alm.add_entries('numbers', tmpDict, lambda x: x)
corrs = self.alm.get_confidence(lex.rscorer, ref='cogid')
self.alm.output('html',
filename=text_type(self.tmp_path('alm')),
confidence=True)
def test_output(self):
self.alm.output('tsv', filename=text_type(self.tmp_path('test')))
self.alm.output('html', filename=text_type(self.tmp_path('test')))
def setUp(self):
WithTempDir.setUp(self)
self.alm = Alignments(test_data('KSL2.qlc'), loans=False, _interactive=False)
class TestAlignments(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.alm = Alignments(test_data('KSL2.qlc'), loans=False, _interactive=False)
def test_ipa2tokens(self):
# iterate over the keys
for key in self.alm: #.get_list(language="Turkish",flat=True):
ipa = self.alm[key, 'ipa']
tokensA = self.alm[key, 'tokensa'].split(' ')
tokensB = self.alm[key, 'tokensb'].split(' ')
new_tokensA = lp.ipa2tokens(ipa, merge_vowels=True)
new_tokensB = lp.ipa2tokens(ipa, merge_vowels=False)
assert tokensA == new_tokensA
assert tokensB == new_tokensB
def test_align(self):
# align all sequences using standard params
self.alm.align()
# iterate and align using the multiple function
for key,value in self.alm.msa['cogid'].items():
# first compare simple alignments
msaA = lp.SCA(value)
msaB = lp.Multiple(value['seqs'])
msaB.prog_align()
assert msaA == msaB
# now compare with different flag
msaA = lp.Multiple([self.alm[idx,'tokensb'] for idx in value['ID']])
msaB = lp.Multiple([''.join(s) for s in value['seqs']],merge_vowels=False)
msaA.lib_align()
msaB.lib_align()
assert msaA == msaB
def test_get_consensus(self):
# align all sequences using standard params
self.alm.align()
tree = TreeNode(
Name='root',
Children=[TreeNode(Name=line.split('\t')[1]) for line in
read_config_file(test_data('KSL2.qlc'))])
self.alm.get_consensus(consensus="consensus", tree=tree)
self.alm.get_consensus(consensus="consensus", classes=True)
self.alm.get_consensus(consensus="consensus")
# check whether Turkish strings are identical
assert self.alm.get_list(
language="Turkish",
entry="consensus",
flat=True
) == \
[''.join(x) for x in self.alm.get_list(
language="Turkish",
entry="tokens",
flat=True
)
]
def test_output(self):
self.alm.align()
self.alm.output('qlc', filename=text_type(self.tmp_path('test')))
self.alm.output('html', filename=text_type(self.tmp_path('test')))
class TestAlignments(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.alm = Alignments(test_data('KSL2.qlc'), loans=False,
_interactive=False)
self.alm.align()
def test_ipa2tokens(self):
# iterate over the keys
for key in self.alm: # get_list(language="Turkish",flat=True):
ipa = self.alm[key, 'ipa']
tokens_a = self.alm[key, 'tokensa'].split(' ')
tokens_b = self.alm[key, 'tokensb'].split(' ')
new_tokens_a = lp.ipa2tokens(ipa, merge_vowels=True,
merge_geminates=False)
new_tokens_b = lp.ipa2tokens(ipa, merge_vowels=False,
merge_geminates=False)
assert tokens_a == new_tokens_a
assert tokens_b == new_tokens_b
def test_align(self):
self.alm.add_entries('cugid', self.alm._ref, lambda x: text_type(x))
self.alm.add_alignments(ref="cugid")
# align all sequences using standard params
self.alm.align(ref="cugid", alignment="alignment2")
assert (self.alm.msa["cugid"]["1"]["ID"] ==
self.alm.msa["cogid"][1]["ID"])
# iterate and align using the multiple function
for key, value in self.alm.msa['cogid'].items():
# first compare simple alignments
msa_a = lp.SCA(value)
msa_b = lp.Multiple(value['seqs'])
msa_b.prog_align()
assert msa_a == msa_b
# now compare with different flag
msa_a = lp.Multiple([self.alm[idx, 'tokensb']
for idx in value['ID']])
msa_b = lp.Multiple([''.join(s) for s in value['seqs']],
merge_vowels=False)
msa_a.lib_align()
msa_b.lib_align()
assert msa_a == msa_b
def test_get_consensus(self):
# align all sequences using standard params
self.alm.get_consensus(consensus="consensus", classes=True)
self.alm.get_consensus(consensus="consensus")
# check whether Turkish strings are identical
self.assertEqual(
self.alm.get_list(language="Turkish", entry="consensus", flat=True),
[''.join(x) for x in
self.alm.get_list(language="Turkish", entry="tokens", flat=True)])
def test_get_confidence(self):
lex = LexStat(test_data('KSL3.qlc'))
tmp_dict = dict([(k, lex[k, 'numbers']) for k in lex])
self.alm.add_entries('numbers', tmp_dict, lambda x: x)
# Run get_confidence to populate the output variable.
# TODO: Check and document side-effects of this.
_ = self.alm.get_confidence(lex.rscorer, ref='cogid')
self.alm.output('html', filename=text_type(self.tmp_path('alm')),
confidence=True)
def test_output(self):
self.alm.output('tsv', filename=text_type(self.tmp_path('test')))
self.alm.output('html', filename=text_type(self.tmp_path('test')))
def alm(test_data):
a = Alignments(str(test_data / 'KSL2.qlc'), loans=False,_interactive=False)
a.align()
return a
class TestAlignments(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.alm = Alignments(test_data('KSL2.qlc'),
loans=False,
_interactive=False)
def test_ipa2tokens(self):
# iterate over the keys
for key in self.alm: #.get_list(language="Turkish",flat=True):
ipa = self.alm[key, 'ipa']
tokensA = self.alm[key, 'tokensa'].split(' ')
tokensB = self.alm[key, 'tokensb'].split(' ')
new_tokensA = lp.ipa2tokens(ipa, merge_vowels=True)
new_tokensB = lp.ipa2tokens(ipa, merge_vowels=False)
assert tokensA == new_tokensA
assert tokensB == new_tokensB
def test_align(self):
# align all sequences using standard params
self.alm.align()
# iterate and align using the multiple function
for key, value in self.alm.msa['cogid'].items():
# first compare simple alignments
msaA = lp.SCA(value)
msaB = lp.Multiple(value['seqs'])
msaB.prog_align()
assert msaA == msaB
# now compare with different flag
msaA = lp.Multiple(
[self.alm[idx, 'tokensb'] for idx in value['ID']])
msaB = lp.Multiple([''.join(s) for s in value['seqs']],
merge_vowels=False)
msaA.lib_align()
msaB.lib_align()
assert msaA == msaB
def test_get_consensus(self):
# align all sequences using standard params
self.alm.align()
tree = TreeNode(Name='root',
Children=[
TreeNode(Name=line.split('\t')[1])
for line in read_config_file(test_data('KSL2.qlc'))
])
self.alm.get_consensus(consensus="consensus", tree=tree)
self.alm.get_consensus(consensus="consensus", classes=True)
self.alm.get_consensus(consensus="consensus")
# check whether Turkish strings are identical
assert self.alm.get_list(
language="Turkish",
entry="consensus",
flat=True
) == \
[''.join(x) for x in self.alm.get_list(
language="Turkish",
entry="tokens",
flat=True
)
]
def test_output(self):
self.alm.align()
self.alm.output('qlc', filename=text_type(self.tmp_path('test')))
self.alm.output('html', filename=text_type(self.tmp_path('test')))