def test_convenience():
info('m')
warning('m')
debug('m')
error('m')
deprecated('o', 'n')
missing_module('m')
file_written('f')
def test_convenience():
info('m')
warning('m')
debug('m')
error('m')
deprecated('o', 'n')
missing_module('m')
file_written('f')
def test_convenience(self):
from lingpy.log import info, warn, debug, error, deprecated, missing_module, file_written
info('m')
warn('m')
debug('m')
error('m')
deprecated('o', 'n')
missing_module('m')
file_written('f')
def test_convenience(self):
from lingpy.log import info, warn, debug, error, deprecated, missing_module, file_written
info('m')
warn('m')
debug('m')
error('m')
deprecated('o', 'n')
missing_module('m')
file_written('f')
def __getitem__(self, key):
key = key.lower()
# first, check whether key is a given concept list
if key in self._keys:
return self._dict[key]
elif key.lower() in ' '.join(self._keys):
matches = []
for k in self._keys:
if key in k:
matches += [k]
if len(matches) == 1:
return self._dict[matches[0]]
else:
log.error(
"Multiple matches could be found: " + ', '.join(matches) + '...')
raise
else:
return
def __getitem__(self, key):
key = key.lower()
# first, check whether key is a given concept list
if key in self._keys:
return self._dict[key]
elif key.lower() in ' '.join(self._keys):
matches = []
for k in self._keys:
if key in k:
matches += [k]
if len(matches) == 1:
return self._dict[matches[0]]
else:
log.error("Multiple matches could be found: " +
', '.join(matches) + '...')
raise
else:
return
def star2qlc(filename, clean_taxnames=False, debug=False):
"""
Converts a file directly output from starling to LingPy-QLC format.
"""
cleant = clean_taxnames or identity
data = csv2list(filename)
# check for strange chars in data due to notepad errors
data[0][0] = data[0][0].replace('\ufeff', '')
# get the header
header = data[0]
# debugging
if debug:
error = False
log.info("Header line has length {0}.".format(len(header)))
for line in data[1:]:
if len(line) != len(header): # pragma: no cover
log.error(
"Error for item {0} with length {1}, expected {2}.".format(
'/'.join(line[0:2]), len(line), len(header)))
error = True
if error: # pragma: no cover
log.error("Errors were found, aborting function call.")
return
else:
log.info("Everything went fine, carrying on with function call.")
# determine language names in header
taxa = []
for i in range(len(header) - 1):
prev = header[i]
post = header[i + 1]
if prev in post and '#' in post:
taxa += [prev]
if len(taxa) == 1:
lngIdx = i
if prev == 'Number':
numIdx = i
if prev == 'Word':
wrdIdx = i
log.info('starling, indices (%s, %s, %s)' % (lngIdx, numIdx, wrdIdx))
log.info('starling, taxa: %s' % taxa)
# start filling in the dictionary
D = {
0: [
'DOCULECT', 'CONCEPT', 'GLOSSID', 'WORDINSOURCE', 'ORTHOGRAPHY',
'IPA', 'COGID'
]
}
idx = 1
cognate_counter = 0
current_concept = ''
cognate_sets = []
for line in data[2:]:
gloss = line[wrdIdx]
gnum = line[numIdx]
# switch to next cognate set if there is a switch in concepts
if current_concept != gloss and len(cognate_sets) != 0:
max_cog = max(cognate_sets)
cognate_counter = max_cog
cognate_sets = []
current_concept = gloss
else:
log.debug('starling, indices (%s, %s, %s)' %
(gloss, current_concept, cognate_counter))
for i in range(lngIdx, len(header), 2):
word = line[i]
if '{' in word:
ipa = word[:word.index('{')].strip()
ortho = word[word.index('{') + 1:word.index('}')].strip()
else:
ipa = word
ortho = word
cogid = int(line[i + 1])
if cogid != 0 and word:
if cogid > 0:
cogid = cogid + cognate_counter
# append cognate sets, essential for raising the counter
cognate_sets += [int(cogid)]
taxon = cleant(header[i])
D[idx] = [taxon, gloss, gnum, word, ortho, ipa, cogid]
idx += 1
# re-iterate through data and reassign cognate sets with negative ids
for k in D:
if k:
cogid = D[k][-1]
if cogid < 0:
cogid = -cognate_counter
cognate_counter += 1
D[k][-1] = cogid
return D
def star2qlc(filename, clean_taxnames=False, debug=False):
"""
Converts a file directly output from starling to LingPy-QLC format.
"""
cleant = clean_taxnames or identity
data = csv2list(filename)
# check for strange chars in data due to notepad errors
data[0][0] = data[0][0].replace('\ufeff', '')
# get the header
header = data[0]
# debugging
if debug:
error = False
log.info("Header line has length {0}.".format(len(header)))
for line in data[1:]:
if len(line) != len(header): # pragma: no cover
log.error("Error for item {0} with length {1}, expected {2}.".format(
'/'.join(line[0:2]), len(line), len(header)))
error = True
if error: # pragma: no cover
log.error("Errors were found, aborting function call.")
return
else:
log.info("Everything went fine, carrying on with function call.")
# determine language names in header
taxa = []
for i in range(len(header) - 1):
prev = header[i]
post = header[i + 1]
if prev in post and '#' in post:
taxa += [prev]
if len(taxa) == 1:
lngIdx = i
if prev == 'Number':
numIdx = i
if prev == 'Word':
wrdIdx = i
log.info('starling, indices (%s, %s, %s)' % (lngIdx, numIdx, wrdIdx))
log.info('starling, taxa: %s' % taxa)
# start filling in the dictionary
D = {0: [
'DOCULECT', 'CONCEPT', 'GLOSSID', 'WORDINSOURCE', 'ORTHOGRAPHY', 'IPA', 'COGID']}
idx = 1
cognate_counter = 0
current_concept = ''
cognate_sets = []
for line in data[2:]:
gloss = line[wrdIdx]
gnum = line[numIdx]
# switch to next cognate set if there is a switch in concepts
if current_concept != gloss and len(cognate_sets) != 0:
max_cog = max(cognate_sets)
cognate_counter = max_cog
cognate_sets = []
current_concept = gloss
else:
if debug:
print(gloss, current_concept, cognate_counter)
for i in range(lngIdx, len(header), 2):
word = line[i]
if '{' in word:
ipa = word[:word.index('{')].strip()
ortho = word[word.index('{') + 1:word.index('}')].strip()
else:
ipa = word
ortho = word
cogid = int(line[i + 1])
if cogid != 0 and word:
if cogid > 0:
cogid = cogid + cognate_counter
else:
pass
# append cognate sets, essential for raising the counter
cognate_sets += [int(cogid)]
taxon = cleant(header[i])
D[idx] = [taxon, gloss, gnum, word, ortho, ipa, cogid]
idx += 1
# re-iterate through data and reassign cognate sets with negative ids
for k in D:
if k:
cogid = D[k][-1]
if cogid < 0:
cogid = -cognate_counter
cognate_counter += 1
D[k][-1] = cogid
return D
