python-modules/alignText.py at master · deborah-powers/python-modules · GitHub

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#!/usr/bin/python3.6
# -*- coding: utf-8 -*-
importrandom

""" ------------------------ créer la matrice des scores ------------------------ """

defsetScorePair (scoreMatrix, score, la, lo):
scoreMatrix [la+lo] =score
scoreMatrix [lo+la] =score

defsetScoreGroup (scoreMatrix, score, letterGroup):
forlainletterGroup:
forloinletterGroup: setScorePair (scoreMatrix, score, la, lo)

defcreateScoreMatrix():
# renvoi un dictionnaire { appariment2char: score }, { 'ab': 5 }
allLetters='aàbcçdeéèêëfghiîïjklmnoôöpqrstuùvwxyz \t\n\r0123456789"\'`/\\=+*-~_.?!:;,¨^°%$@&#<>{}()[]'
alphabet='aàbcçdeéèêëfghiîïjklmnoôöpqrstuùvwxyz'
voyels='aàeéèêëiîïoôöuùy';
consomns='bcçdfghjklmnpqrstvwxz'
numbers='0123456789'
spaces=' \t\n\r';
quotes='"\'`';
brackets='{}()[]';
tirets='_-~';
points='.?!:;,'
mathOperator='+-*/^<>='
others='^°%$@&#'
scoreMatrix= {}
setScoreGroup (scoreMatrix, 5, allLetters)
setScoreGroup (scoreMatrix, 4, alphabet)
setScoreGroup (scoreMatrix, 3, voyels)
setScoreGroup (scoreMatrix, 3, consomns)
setScoreGroup (scoreMatrix, 3, numbers)
setScoreGroup (scoreMatrix, 3, points)
setScoreGroup (scoreMatrix, 3, tirets)
setScoreGroup (scoreMatrix, 2, spaces)
setScoreGroup (scoreMatrix, 2, quotes)
# cas particuliers
setScorePair (scoreMatrix, 2, '/', '\\')
setScorePair (scoreMatrix, 2, '(', '[')
setScorePair (scoreMatrix, 2, ')', ']')
setScorePair (scoreMatrix, 1, 'a', 'à')
setScorePair (scoreMatrix, 1, 'u', 'ù')
setScorePair (scoreMatrix, 1, 'u', 'y')
setScorePair (scoreMatrix, 1, 'c', 'ç')
setScorePair (scoreMatrix, 1, 'i', 'î')
setScorePair (scoreMatrix, 1, 'i', 'ï')
setScorePair (scoreMatrix, 1, 'î', 'ï')
setScorePair (scoreMatrix, 1, 'i', 'y')
setScorePair (scoreMatrix, 1, 'o', 'ô')
setScorePair (scoreMatrix, 1, 'o', 'ö')
setScorePair (scoreMatrix, 1, 'ô', 'ö')
setScorePair (scoreMatrix, 1, 'e', 'é')
setScorePair (scoreMatrix, 1, 'e', 'è')
setScorePair (scoreMatrix, 1, 'e', 'ê')
setScorePair (scoreMatrix, 1, 'e', 'ë')
setScorePair (scoreMatrix, 1, 'e', '€')
setScorePair (scoreMatrix, 1, 'é', 'è')
setScorePair (scoreMatrix, 1, 'é', 'ê')
setScorePair (scoreMatrix, 1, 'é', 'ë')
setScorePair (scoreMatrix, 1, 'è', 'ê')
setScorePair (scoreMatrix, 1, 'è', 'ë')
setScorePair (scoreMatrix, 1, 'ê', 'ë')
forlinallLetters: scoreMatrix[l+l] =0
returnscoreMatrix

"""
0 identiques
1 variantes de lettres
2 lettres souvent confondues
3 lettres de la même catégories
4 lettres de l'alphabet
5 le reste
"""
""" ------------------------ créer la matrice d'alignement ------------------------ """

scoreGapOpen=2
scoreGapFill=2
scoreMatrix=createScoreMatrix()

definitAliMatrix (textA, textI):
# les textes commencent déjà par un caractère symbolisant le gap
lenI=len (textI)
aliMatrix=[]
forcharintextA:
aliMatrix.append ([])	# initier la matrice vide
forchirintextI: aliMatrix[-1].append ((scoreGapOpen, 3))
rangeO=range (1, len (textA))
forainrangeO: aliMatrix[a][0] =( aliMatrix[a-1][0][0] +scoreGapOpen, 3)
rangeO=range (1, lenI)
foriinrangeO: aliMatrix[0][i] =( aliMatrix[0][i-1][0] +scoreGapOpen, 3)
returnaliMatrix

defgetPosScoreTrioMin (scoreTrio):
score=scoreTrio[0]
pos=0
ifscoreTrio[1] <score:
score=scoreTrio[1]
pos=1
ifscoreTrio[2] <score:
score=scoreTrio[2]
pos=2
returnscore, pos

defcomputeCaseScore (a,i, textA, textI, aliMatrix):
scoreTrio=[]
scoreTrio.append (aliMatrix[a-1][i][0] +scoreGapFill)	# gap en i aligné en face de la lettre de a
scoreTrio.append (aliMatrix[a-1][i-1][0] +scoreMatrix [textA[a] +textI[i]])
scoreTrio.append (aliMatrix[a][i-1][0] +scoreGapFill)	# gap en a aligné en face de la lettre de i
#	scoreTrio.append (aliMatrix[0][i][0])	# gap en a aligné en face de la lettre de i
returngetPosScoreTrioMin (scoreTrio)

defcreateAliMatrix (textA, textI):
textA='#'+textA## symbolise le gap
textI='#'+textI
aliMatrix=initAliMatrix (textA, textI)
lenA=len (textA)
lenI=len (textI)
rangeA=range (1, lenA)
rangeI=range (1, lenI)
forainrangeA:
foriinrangeI: aliMatrix[a][i] =computeCaseScore (a,i, textA, textI, aliMatrix)
returnaliMatrix

defupwalkAliMatrix (textA, textI, aliMatrix):
textA='#'+textA## symbolise le gap
textI='#'+textI
a=len (textA) -1
i=len (textI) -1
textAnv=""
textInv=""
whilea>0andi>0:
ifaliMatrix[a][i][1] ==1:	# alignement
textAnv=textA[a] +textAnv
textInv=textI[i] +textInv
a-=1
i-=1
elifaliMatrix[a][i][1] ==0:	# gap dans i
textAnv=textA[a] +textAnv
textInv='_'+textInv
a-=1
elifaliMatrix[a][i][1] ==2:	# gap dans a
textAnv='_'+textAnv
textInv=textI[i] +textInv
i-=1
print (textA)
print (textI)
#	textAnv = textAnv[::-1]
print (textAnv)
print (textInv)
returntextAnv, textInv

defalignText (textA, textI):
aliMatrix=createAliMatrix (textA, textI)
textAnv, textInv=upwalkAliMatrix (textA, textI, aliMatrix)

alignText ('zrzog,el', 'nanczk,vl;')