README.md

Feature-Based Alignment Analyses with LingPy and CLTS (2)

Requirements (can all be installed with PIP)

• lingpy
• pyclts

Run code

python features2.py

More information

• https://calc.hypotheses.org

covington.psa

COVINGTON
yo/je
Spanish.........	j	o
French..........	ʒ	ə
# 4.0

tu/tu
Spanish.........	t	u
French..........	t	y
# 15.0

nosotros/nous
Spanish.........	n	o	s	o	t	r	o	s
French..........	n	u	-	-	-	-	-	-
# 14.0

quién/qui
Spanish.........	k	j	e	n
French..........	k	-	i	-
# 9.2

qué/quoi
Spanish.........	k	-	e
French..........	k	w	a
# 9.2

todos/tous
Spanish.........	t	o	d	o	s
French..........	t	u	-	-	-
# 14.0

una/une
Spanish.........	u	n	a
French..........	y	n	-
# 15.0

dos/deux
Spanish.........	d	o	s
French..........	d	ø	-
# 15.0

tres/troix
Spanish.........	t	r	-	e	s
French..........	t	r	w	a	-
# 19.2

hombre/homme
Spanish.........	o	m	b	r	e
French..........	o	m	-	-	-
# 15.0

árbol/arbre
Spanish.........	a	r	b	o	l	-
French..........	a	r	b	-	r	ə
# 25.0

plume/plume
Spanish.........	p	l	u	m	a
French..........	p	l	y	m	-
# 35.0

cabeza/cap
Spanish.........	k	a	b	e	θ	a
French..........	k	a	p	-	-	-
# 25.0

boca/bouche
Spanish.........	b	o	k	a
French..........	b	u	ʃ	-
# 16.0

pie/pied
Spanish.........	p	j	e
French..........	p	j	e
# 25.0

corazón/coeur
Spanish.........	k	o	r	a	θ	o	n
French..........	k	ø	r	-	-	-	-
# 25.0

ver/voir
Spanish.........	b	-	e	r
French..........	v	w	a	r
# 16.0

venir/venir
Spanish.........	b	e	n	i	r
French..........	v	ə	n	i	r
# 36.0

decir/dire
Spanish.........	d	e	θ	i	r
French..........	d	-	-	i	r
# 21.0

pobre/pauvre
Spanish.........	p	o	b	r	e
French..........	p	o	v	r	ə
# 36.0

this/dieses
English.........	ð	i	s	-	-
German..........	d	iː	z	e	s
# 21.0

that/das
English.........	ð	æ	t
German..........	d	a	s
# 12.0

what/was
English.........	w	a	t
German..........	v	a	s
# 13.0

not/nicht
English.........	n	a	-	t
German..........	n	i	x	t
# 19.6

long/lang
English.........	l	o	ŋ
German..........	l	a	ŋ
# 24.0

man/Mann
English.........	m	æ	n
German..........	m	a	n
# 24.0

flesh/Fleisch
English.........	f	l	e	ʃ
German..........	f	l	ai	ʃ
# 34.0

blood/Blut
English.........	b	l	ə	d
German..........	b	l	uː	t
# 34.0

feather/Feder
English.........	f	e	ð	ə	r
German..........	f	eː	d	ə	r
# 36.0

hair/Haar
English.........	h	æ	r
German..........	h	aː	r
# 24.0

ear/Ohr
English.........	iː	r
German..........	oː	r
# 14.0

eye/Auge
English.........	ai	-	-
German..........	au	g	ə
# 5.0

nose/Nase
English.........	n	ou	z	-
German..........	n	aː	z	ə
# 24.0

mouth/Mund
English.........	m	au	-	θ
German..........	m	u	n	t
# 15.6

tongue/Zunge
English.........	t	ə	ŋ	-
German..........	ʦ	u	ŋ	ə
# 20.0

foot/Fuß
English.........	f	u	t
German..........	f	uː	s
# 17.0

knee/Knie
English.........	-	n	iː
German..........	k	n	iː
# 15.0

hand/Hand
English.........	h	æ	n	d
German..........	h	a	n	t
# 34.0

hart/Herz
English.........	h	a	r	t
German..........	h	e	r	ʦ
# 30.0

liver/Leber
English.........	l	i	v	ə	r
German..........	l	eː	b	ə	r
# 35.0

and/ante
English.........	æ	n	d	-
Latin...........	a	n	t	e
# 24.0

at/at
English.........	æ	t
Latin...........	a	t
# 14.0

blow/flare
English.........	b	l	ou	-	-
Latin...........	f	l	aː	r	e
# 20.0

ear/auris
English.........	iː	-	r	-	-
Latin...........	a	w	r	i	s
# 9.2

eat/edere
English.........	iː	t	-	-	-
Latin...........	e	d	e	r	e
# 14.0

fish/piscis
English.........	f	i	ʃ	-	-	-
Latin...........	p	i	s	k	i	s
# 21.0

flow/flu.ere
English.........	f	l	ou	-	-	-
Latin...........	f	l	u	e	r	e
# 24.0

star/stella
English.........	s	t	a	r	-
Latin...........	s	t	eː	lː	a
# 28.0

full/plenus
English.........	f	u	l	-	-	-	-
Latin...........	p	-	l	eː	n	u	s
# 12.0

grass/gramen
English.........	g	r	æ	s	-	-
Latin...........	g	r	aː	m	e	n
# 24.0

heart/cordis
English.........	h	a	r	t	-	-
Latin...........	k	o	r	d	i	s
# 24.0

horn/cornu
English.........	h	o	r	n	-
Latin...........	k	o	r	n	uː
# 25.0

I/ego
English.........	ai	-	-
Latin...........	e	g	o
# 4.0

knee/genu
English.........	-	-	n	iː
Latin...........	g	e	n	uː
# 14.0

mother/mater
English.........	m	ə	ð	ə	r
Latin...........	m	aː	t	e	r
# 35.0

mountain/mons
English.........	m	au	n	t	ə	n
Latin...........	m	oː	n	s	-	-
# 26.0

new/novus
English.........	n	iu	-	-	-
Latin...........	n	o	w	u	s
# 19.2

name/nomen
English.........	n	a	m	e	-
Latin...........	n	o	m	e	n
# 0.0

one/unus
English.........	w	ə	n	-	-
Latin...........	-	uː	n	u	s
# 12.8

round/rotundus
English.........	r	au	-	-	n	d	-	-
Latin...........	r	o	t	u	n	d	u	s
# 27.12

sew/suere
English.........	s	ou	-	-	-
Latin...........	s	u	e	r	e
# 14.0

sit/sedere
English.........	s	i	t	-	-	-
Latin...........	s	eː	d	e	r	e
# 24.0

three/tres
English.........	θ	r	iː	-
Latin...........	t	r	eː	s
# 20.0

tooth/dentis
English.........	t	u	-	θ	-	-
Latin...........	d	e	n	t	i	s
# 20.0

thin/tenuis
English.........	θ	i	n	-	-	-
Latin...........	t	e	n	w	i	s
# 20.0

kiinwaawa/kenuaq
Fox.............	k	iː	n	w	aː	w	a
Menomini........	k	e	n	u	a	ʔ	-
# 24.0

niina/nenah
Fox.............	n	iː	n	a	-
Menomini........	n	e	n	a	h
# 29.0

naapeewa/naapeew
Fox.............	n	aː	p	eː	w	a
Menomini........	n	aː	p	ɛː	w	-
# 40.0

waapimini/waapemen
Fox.............	w	aː	p	i	m	i	n	i
Menomini........	w	aː	p	e	m	e	n	-
# 53.0

nameesa/nameeqs
Fox.............	n	a	m	eː	-	s	a
Menomini........	n	a	m	ɛː	ʔ	s	-
# 35.2

okimaawa/okeemaaw
Fox.............	o	k	i	m	aː	w	a
Menomini........	o	k	eː	m	aː	w	-
# 44.0

šišiipa/seeqsep
Fox.............	ʃ	iː	-	ʃ	iː	p	a
Menomini........	s	eː	ʔ	s	e	p	-
# 33.2

ahkohkwa/ahkeeh
Fox.............	a	h	k	o	h	k	w	a
Menomini........	a	h	k	ɛː	h	-	-	-
# 39.0

pemaatesiweni/pemaateswen
Fox.............	p	e	m	aː	t	e	s	i	w	e	n	i
Menomini........	p	e	m	aː	t	e	s	e	w	e	n	-
# 84.0

asenya/aqsen
Fox.............	a	-	s	e	n	j	a
Menomini........	a	ʔ	s	ɛ	n	-	-
# 25.2

δίδωμι/do
Old_Greek.......	d	i	d	oː	m	i
Latin...........	-	-	d	oː	-	-
# 15.0

θυγατηρ/Tochter
Old_Greek.......	tʰ	u	g	a	t	eː	r
German..........	t	o	x	-	t	ə	r
# 39.2

daughter/θυγατηρ
English.........	d	ɔː	-	-	t	ə	r
Old_Greek.......	tʰ	u	g	a	t	eː	r
# 32.12

ager/ajras
Latin...........	a	g	e	r	-	-
Sanskrit........	a	ʥ	-	r	a	s
# 17.0

bharāmi/φέρθ
Sanskrit........	bʱ	a	r	aː	m	i
Old_Greek.......	pʰ	e	r	o	-	-
# 28.0

centum/ἕκατον
Latin...........	-	-	k	e	n	t	u	m
Old_Greek.......	h	e	k	a	-	t	o	n
# 24.6

centum/satəm
Latin...........	k	e	n	t	u	m
Iranian.........	s	a	-	t	ə	m
# 25.6

features2.py

from pyclts.transcriptionsystem import TranscriptionSystem
from itertools import combinations
from lingpy.algorithm.cython import malign
from lingpy import *

def score_sounds(
        a, 
        b, 
        features=None, 
        classes=None, 
        bipa=None
        ):
    """
    Score sounds with Hamming distance from feature system.
    """
    # load bipa object
    bipa = bipa or TranscriptionSystem('bipa')

    # define the features
    features = features or {
        "consonant": list(
            bipa['t'].featuredict),
        "vowel": list(
            bipa['a'].featuredict),
        "tone": list(
            bipa['⁵⁵'].featuredict)
        }
    # define base score for the classes
    classes = classes or {
        "consonant": 1, 
        "vowel": 1, 
        "tone": 1
        }
    
    # convert sounds to transcription system
    sA, sB = bipa(a+' '+b)
    
    # check for diphthongs or clusters
    if hasattr(sA, 'from_sound'):
        sA = sA.from_sound
    if hasattr(sB, 'from_sound'):
        sB = sB.from_sound
    
    # return -10 if classes don't match
    if sA.type != sB.type:
        return -10

    # base score is the number of features
    sim = len(features[sA.type])

    # normalization factor
    normalize = classes[sA.type] / sim

    # return in case of identity
    if a == b:
        return sim * normalize
    
    # reduce similarity in case of mismatch
    for feature in features[sA.type]:
        if sA.featuredict[feature] != sB.featuredict[feature]:
            sim -= 1
    return sim * normalize


def get_scorer(
        letters, 
        bipa=None, 
        classes=None, 
        features=None
        ):
    """
    Retrieve a scoring dictionary for alignment algorithms.
    """
    # load bipa object
    bipa = bipa or TranscriptionSystem('bipa')

    # define the features
    features = features or {
        "consonant": list(
            bipa['t'].featuredict),
        "vowel": list(
            bipa['a'].featuredict),
        "tone": list(
            bipa['⁵⁵'].featuredict)
        }
    # define base score for the classes
    classes = classes or {
        "consonant": 1, 
        "vowel": 1, 
        "tone": 1
        }
    
    scorer = {}
    bipa = bipa or TranscriptionSystem('bipa')
    for a, b in combinations(letters, r=2):
        scorer[a, b] = scorer[b, a] = score_sounds(a, b, bipa=bipa)
        scorer[a, a] = score_sounds(a, a, bipa=bipa)
        scorer[b, b] = score_sounds(b, b, bipa=bipa)

    return scorer


def feature_align(seqA, seqB, mode='global', gop=-1):
    if mode == 'global':
        align = malign.nw_align
    elif mode == 'local':
        align = malign.sw_align

    scorer = get_scorer(list(set(seqA+seqB)))

    return align(seqA, seqB, scorer, gop)

# test the aligment procedure    
seqA = 'tʰ ɔ x t ɐ'.split()
seqB = 'd ɔː t ə r'.split()
almA, almB, score = feature_align(seqA, seqB)
print('\t'.join(almA))
print('\t'.join(almB))
print('{0:.2f}'.format(score))

# test the alignment on the covington package
psa = PSA('covington.psa')
scores = []
for i, (seqA, seqB) in enumerate(psa.tokens):
    almA, almB, score = feature_align(seqA, seqB)
    if almA == psa.alignments[i][0] and almB == psa.alignments[i][1]:
        scores += [1]
    else:
        scores += [0]
print('{0:.2f}'.format(sum(scores)/len(scores)))
print(sum(scores))