alignment for profiles
This commit is contained in:
Céline Mercier
3924
src/obitools/align/_gprofilenws.c
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3924
src/obitools/align/_gprofilenws.c
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src/obitools/align/_gprofilenws.pxd
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src/obitools/align/_gprofilenws.pxd
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from _profilenws cimport *
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cdef class GProfileNWS(ProfileNWS):
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cdef double matchScore(self,int h, int v)
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cdef object alignment1
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cdef object alignment2
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#cdef double doAlignment(self) except? 0
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src/obitools/align/_gprofilenws.pyx
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src/obitools/align/_gprofilenws.pyx
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'''
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Created on 16 Feb. 2011
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@author: celine
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'''
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#@PydevCodeAnalysisIgnore
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from _gprofilenws cimport *
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cdef class GProfileNWS(ProfileNWS):
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cdef double matchScore(self,int h, int v):
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cdef double pmatch
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cdef double* hp = self.hProf.frequency
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cdef double* vp = self.vProf.frequency
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cdef int hl = self.hProf.length
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cdef int vl = self.vProf.length
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h-=1
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v-=1
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pmatch = hp[h]*vp[v] + \
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hp[h+hl]*vp[v+vl] + \
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hp[h+2*hl]*vp[v+2*vl] + \
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hp[h+3*hl]*vp[v+3*vl] + \
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hp[h+4*hl]*vp[v+4*vl] + \
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hp[h+5*hl]*vp[v+5*vl]
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return self._match * pmatch + (1-pmatch) * self._mismatch
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def __call__(self,pseudocounts=0):
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cdef list hgaps=[]
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cdef list vgaps=[]
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cdef list b
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cdef int hp
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cdef int vp
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cdef int rp
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cdef int lenh=0
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cdef int lenv=0
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cdef int h,v,p
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cdef int i
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cdef object ali
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cdef double score
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cdef DNAProfile newProfile1
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cdef DNAProfile newProfile2
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cdef DNAProfile horizontalSeq=self.horizontalSeq
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cdef DNAProfile verticalSeq=self.verticalSeq
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if self._needToCompute():
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score = self.doAlignment()
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self.backtrack()
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sum = 0
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for p in xrange(self.path.length) :
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v = self.path.path[p]
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if v == 0 :
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sum += 1
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else :
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sum += abs(v)
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newProfile1 = DNAProfile(size=sum,pseudo=pseudocounts)
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newProfile1.profile.weight = horizontalSeq.profile.weight
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newProfile2 = DNAProfile(size=sum,pseudo=pseudocounts)
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newProfile2.profile.weight = verticalSeq.profile.weight
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hp=horizontalSeq.profile.length-1
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vp=verticalSeq.profile.length-1
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rp1=newProfile1.profile.length-1
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rp2=newProfile2.profile.length-1
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for i in range(self.path.length):
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p=self.path.path[i]
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for i in range(self.path.length):
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p=self.path.path[i]
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if p==0:
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newProfile1.A[rp1] = horizontalSeq.A[hp]
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newProfile1.C[rp1] = horizontalSeq.C[hp]
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newProfile1.G[rp1] = horizontalSeq.G[hp]
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newProfile1.T[rp1] = horizontalSeq.T[hp]
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newProfile1.Og[rp1] = horizontalSeq.Og[hp]
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newProfile1.Eg[rp1] = horizontalSeq.Eg[hp]
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newProfile2.A[rp2] = verticalSeq.A[vp]
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newProfile2.C[rp2] = verticalSeq.C[vp]
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newProfile2.G[rp2] = verticalSeq.G[vp]
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newProfile2.T[rp2] = verticalSeq.T[vp]
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newProfile2.Og[rp2] = verticalSeq.Og[vp]
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newProfile2.Eg[rp2] = verticalSeq.Eg[vp]
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hp-=1
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vp-=1
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rp1-=1
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rp2-=1
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elif p>0:
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for x in xrange(p-1) :
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newProfile1.A[rp1] = horizontalSeq.A[hp]
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newProfile1.C[rp1] = horizontalSeq.C[hp]
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newProfile1.G[rp1] = horizontalSeq.G[hp]
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newProfile1.T[rp1] = horizontalSeq.T[hp]
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newProfile1.Og[rp1] = horizontalSeq.Og[hp]
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newProfile1.Eg[rp1] = horizontalSeq.Eg[hp]
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newProfile2.Eg[rp2] = verticalSeq.profile.weight
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hp-=1
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rp1-=1
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rp2-=1
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newProfile1.A[rp1] = horizontalSeq.A[hp]
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newProfile1.C[rp1] = horizontalSeq.C[hp]
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newProfile1.G[rp1] = horizontalSeq.G[hp]
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newProfile1.T[rp1] = horizontalSeq.T[hp]
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newProfile1.Og[rp1] = horizontalSeq.Og[hp]
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newProfile1.Eg[rp1] = horizontalSeq.Eg[hp]
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newProfile2.Og[rp2] = verticalSeq.profile.weight
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hp-=1
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rp1-=1
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rp2-=1
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else:
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for x in xrange(abs(p)-1) :
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newProfile2.A[rp2] = verticalSeq.A[vp]
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newProfile2.C[rp2] = verticalSeq.C[vp]
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newProfile2.G[rp2] = verticalSeq.G[vp]
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newProfile2.T[rp2] = verticalSeq.T[vp]
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newProfile2.Og[rp2] = verticalSeq.Og[vp]
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newProfile2.Eg[rp2] = verticalSeq.Eg[vp]
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newProfile1.Eg[rp1] = horizontalSeq.profile.weight
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vp-=1
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rp1-=1
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rp2-=1
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newProfile2.A[rp2] = verticalSeq.A[vp]
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newProfile2.C[rp2] = verticalSeq.C[vp]
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newProfile2.G[rp2] = verticalSeq.G[vp]
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newProfile2.T[rp2] = verticalSeq.T[vp]
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newProfile2.Og[rp2] = verticalSeq.Og[vp]
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newProfile2.Eg[rp2] = verticalSeq.Eg[vp]
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newProfile1.Og[rp1] = horizontalSeq.profile.weight
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vp-=1
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rp1-=1
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rp2-=1
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self.alignment1 = newProfile1
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self.alignment2 = newProfile2
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ali1=DNAProfile(self.alignment1,pseudo=pseudocounts)
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ali2=DNAProfile(self.alignment2,pseudo=pseudocounts)
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return ali1, ali2
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