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