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()
def alm(test_data):
a = Alignments(str(test_data / 'KSL2.qlc'), loans=False,_interactive=False)
a.align()
return a
