def run(args):
ds = Dataset()
try:
part = Partial(
ds.dir.joinpath('workflow', 'D_Chen_partial.bin.tsv').as_posix())
except:
part = Partial(ds.dir.joinpath('workflow',
'D_Chen_subset.tsv').as_posix(),
segments='tokens')
part.get_partial_scorer(runs=10000)
part.output('tsv',
filename=ds.dir.joinpath('workflow',
'D_Chen_partial.bin').as_posix(),
ignore=[],
prettify=False)
args.log.info('[i] saved the scorer')
finally:
part.partial_cluster(method='lexstat',
threshold=0.55,
ref='cogids',
mode='global',
gop=-2,
cluster_method='infomap')
part.output('tsv',
filename=ds.dir.joinpath('workflow',
'D_Chen_partial').as_posix(),
prettify=False)
def run(args):
ds = Dataset(args)
wl = Wordlist.from_cldf(
str(ds.cldf_specs().dir.joinpath('cldf-metadata.json')))
D = {0: [x for x in wl.columns]}
for idx in wl:
if wl[idx, 'tokens']:
D[idx] = wl[idx]
part = Partial(D, check=True)
part.get_partial_scorer(runs=10000)
part.partial_cluster(method='lexstat',
threshold=0.45,
ref="cogids",
cluster_method='infomap')
alms = Alignments(part, ref='cogids', fuzzy=True)
alms.align()
alms.output('tsv', filename="chin-aligned")
class Tests(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.part = Partial(test_data('partial_cognates.tsv'),
segments='segments',
split_on_tones=True)
self.part2 = Partial(test_data('partial_cognates-scored.tsv'),
segments='segments')
def test__get_slices(self):
a = _get_slices(list('ba²te²'), split_on_tones=True)
b = _get_slices(list('ba²te²'), split_on_tones=False)
assert a[0][1] == 3
assert b[0][1] == 6
def test_get_partial_scorer(self):
self.part2.get_partial_scorer(runs=10)
def test_get_partial_matrices(self):
for method in ['upgma', 'single', 'complete', 'ward', 'mcl']:
matrix = list(
self.part._get_partial_matrices(cluster_method=method,
concept="bird"))[0]
assert isinstance(matrix[0][0], (float, int))
if lingpy.algorithm.extra.igraph:
for concept, tracer, matrix in self.part._get_partial_matrices(
cluster_method='infomap'):
assert isinstance(concept, text_type)
assert [x[0] for x in tracer]
def test_partial_cluster(self):
assert_raises(ValueError,
self.part.partial_cluster,
cluster_method='upgmu')
self.part.partial_cluster(method='sca',
threshold=0.45,
split_on_tones=True,
post_processing=False,
cluster_method='infomap' if
lingpy.algorithm.extra.igraph else 'upgma',
ref='parts1')
self.part.partial_cluster(method='sca',
threshold=0.45,
post_processing=False,
cluster_method='mcl',
ref='parts2',
split_on_tones=True)
self.part.partial_cluster(method='sca',
threshold=0.45,
split_on_tones=True,
post_processing=False,
cluster_method='upgma',
ref='parts3')
self.part2.partial_cluster(method='lexstat',
threshold=0.6,
cluster_method='single',
post_processing=True,
imap_mode=False,
split_on_tones=True,
ref='parts4')
# high threshold to trigger post-processing movement
self.part.partial_cluster(method='sca',
threshold=0.9,
split_on_tones=True,
cluster_method='single',
post_processing=True,
imap_mode=False,
ref='parts5')
assert self.part[9, 'parts3'][0] == self.part[10, 'parts3'][0]
assert self.part2[8, 'parts4'][1] == self.part2[10, 'parts4'][1]
def test_add_cognate_ids(self):
self.part.partial_cluster(method='sca',
threshold=0.45,
split_on_tones=True,
cluster_method='upgma',
ref='parts3')
self.part.add_cognate_ids('parts3', 'cogs1', idtype='strict')
self.part.add_cognate_ids('parts3', 'cogs2', idtype='loose')
assert self.part[9, 'cogs1'] == self.part[10, 'cogs1']
assert_raises(ValueError,
self.part.add_cognate_ids,
'parts3',
'cogs1',
idtype='dummy')
from lingpy import *
from lingpy.compare.partial import Partial
from sys import argv
if 'all' in argv:
fname='A_Chen_'
else:
fname='D_Chen_'
try:
part = Partial(fname+'partial.bin.tsv')
except:
part = Partial(fname+'subset.tsv', segments='tokens')
print('[i] loaded the file')
part.get_partial_scorer(runs=10000)
part.output('tsv', filename=fname+'partial.bin', ignore=[], prettify=False)
print('[i] saved the scorer')
finally:
part.partial_cluster(
method='lexstat',
threshold=0.55,
ref='cogids',
mode='global',
gop=-2,
cluster_method='infomap'
)
part.output('tsv', filename=fname+'partial', prettify=False)
