New command: obi ngsfilter
This commit is contained in:
Celine Mercier
11
python/obitools3/align/_freeendgap.pxd
Executable file
11
python/obitools3/align/_freeendgap.pxd
Executable file
@ -0,0 +1,11 @@
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#cython: language_level=3
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from ._nws cimport *
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cdef class FreeEndGap(NWS):
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cdef double xsmax
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cdef int xmax
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cdef double doAlignment(self) except? 0
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160
python/obitools3/align/_freeendgap.pyx
Executable file
160
python/obitools3/align/_freeendgap.pyx
Executable file
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#cython: language_level=3
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'''
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Created on 6 Nov. 2009
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@author: coissac
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'''
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cdef class FreeEndGap(NWS):
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def __init__(self,match=4,mismatch=-6,opengap=-8,extgap=-2):
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NWS.__init__(self,match,mismatch,opengap,extgap)
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self.xsmax=0
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self.xmax=0
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cdef double doAlignment(self) except? 0:
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cdef int i # vertical index
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cdef int j # horizontal index
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cdef int idx
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cdef int idx0
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cdef int idx1
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cdef int jump
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cdef int delta
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cdef double score
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cdef double scoremax
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cdef int path
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assert self.hSeq.length > self.vSeq.length, \
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"Sequence B must be shorter than sequence A"
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if self.needToCompute:
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self.allocate()
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self.reset()
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self.xsmax=0
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self.xmax=0
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for j in range(1,self.hSeq.length+1):
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idx = self.index(j,0)
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self.matrix.matrix[idx].score = 0
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self.matrix.matrix[idx].path = j
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for i in range(1,self.vSeq.length+1):
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idx = self.index(0,i)
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self.matrix.matrix[idx].score = self._opengap + (self._extgap * (i-1))
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self.matrix.matrix[idx].path = -i
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idx0=self.index(-1,0)
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idx1=self.index(0,1)
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for i in range(1,self.vSeq.length+1):
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idx0+=1
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idx1+=1
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for j in range(1,self.hSeq.length+1):
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# 1 - came from diagonal
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#idx = self.index(j-1,i-1)
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idx = idx0
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# print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
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scoremax = self.matrix.matrix[idx].score + \
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self.matchScore(j,i)
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path = 0
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# print "so=%f sd=%f sm=%f" % (self.matrix.matrix[idx].score,self.matchScore(j,i),scoremax),
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# 2 - open horizontal gap
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# idx = self.index(j-1,i)
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idx = idx1 - 1
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score = self.matrix.matrix[idx].score+ \
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self._opengap
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if score > scoremax :
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scoremax = score
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path = +1
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# 3 - open vertical gap
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# idx = self.index(j,i-1)
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idx = idx0 + 1
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score = self.matrix.matrix[idx].score + \
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self._opengap
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if score > scoremax :
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scoremax = score
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path = -1
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# 4 - extend horizontal gap
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jump = self.matrix.bestHJump[i]
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if jump >= 0:
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idx = self.index(jump,i)
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delta = j-jump
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score = self.matrix.matrix[idx].score + \
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self._extgap * delta
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if score > scoremax :
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scoremax = score
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path = delta+1
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# 5 - extend vertical gap
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jump = self.matrix.bestVJump[j]
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if jump >= 0:
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idx = self.index(j,jump)
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delta = i-jump
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score = self.matrix.matrix[idx].score + \
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self._extgap * delta
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if score > scoremax :
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scoremax = score
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path = -delta-1
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# idx = self.index(j,i)
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idx = idx1
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self.matrix.matrix[idx].score = scoremax
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self.matrix.matrix[idx].path = path
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if path == -1:
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self.matrix.bestVJump[j]=i
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elif path == +1 :
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self.matrix.bestHJump[i]=j
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if i==self.vSeq.length and scoremax > self.xsmax:
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self.xsmax=scoremax
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self.xmax=j
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idx0+=1
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idx1+=1
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self.sequenceChanged=False
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self.scoreChanged=False
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return self.xsmax
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cdef void backtrack(self):
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#cdef list path=[]
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cdef int i
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cdef int j
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cdef int p
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self.doAlignment()
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j=self.xmax
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i=self.vSeq.length
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self.path=allocatePath(i,j+1,self.path)
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if self.xmax<self.hSeq.length:
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self.path.path[self.path.length]=self.hSeq.length-self.xmax
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self.path.length+=1
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while (i or j):
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p=self.matrix.matrix[self.index(j,i)].path
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self.path.path[self.path.length]=p
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self.path.length+=1
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#path.append(p)
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if p==0:
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i-=1
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j-=1
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elif p < 0:
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i+=p
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else:
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j-=p
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#path.reverse()
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#reversePath(self.path)
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self.path.hStart=0
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self.path.vStart=0
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#return 0,0,path
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7
python/obitools3/align/_freeendgapfm.pxd
Executable file
7
python/obitools3/align/_freeendgapfm.pxd
Executable file
@ -0,0 +1,7 @@
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#cython: language_level=3
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from ._freeendgap cimport *
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cdef class FreeEndGapFullMatch(FreeEndGap):
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cdef double matchScore(self,int h, int v)
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18
python/obitools3/align/_freeendgapfm.pyx
Executable file
18
python/obitools3/align/_freeendgapfm.pyx
Executable file
@ -0,0 +1,18 @@
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#cython: language_level=3
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'''
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Created on 6 Nov. 2009
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@author: coissac
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'''
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cdef class FreeEndGapFullMatch(FreeEndGap):
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cdef double matchScore(self,int h, int v):
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cdef double score
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if iupacMatch(self.hSeq.sequence[h-1],self.vSeq.sequence[v-1]):
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score=self._match
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else:
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score=self._mismatch
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return score
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@ -6,8 +6,6 @@ Created on 6 Nov. 2009
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@author: coissac
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'''
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from ._rassemble cimport *
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cdef class RightDirectAssemble(NWS):
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410
python/obitools3/commands/ngsfilter.pyx
Normal file
410
python/obitools3/commands/ngsfilter.pyx
Normal file
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#cython: language_level=3
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.dms import DMS
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from obitools3.dms.view import RollbackException
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from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
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from obitools3.dms.column.column cimport Column, Column_line
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from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN
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from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t, OBI_QUAL
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from obitools3.apps.optiongroups import addSequenceInputOption, addMinimalOutputOption
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from obitools3.uri.decode import open_uri
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from obitools3.apps.config import logger
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from obitools3.align._freeendgapfm import FreeEndGapFullMatch
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from obitools3.dms.obiseq cimport Nuc_Seq, Nuc_Seq_Stored
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from functools import reduce, cmp_to_key
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import math
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from curses.ascii import SO
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__title__="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"
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def addOptions(parser):
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addSequenceInputOption(parser)
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addMinimalOutputOption(parser)
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group = parser.add_argument_group('obi ngsfilter specific options')
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group.add_argument('-t','--info-view',
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action="store", dest="ngsfilter:info_view",
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metavar="<URI>",
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type=str,
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default=None,
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help="URI to the view containing the samples definition (with tags, primers, sample names,...)")
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group.add_argument('-u','--unidentified',
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action="store", dest="ngsfilter:unidentified",
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metavar="<URI>",
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type=str,
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default=None,
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help="URI to the view used to store the sequences unassigned to any sample")
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group.add_argument('-e','--error',
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action="store", dest="ngsfilter:error",
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metavar="###",
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type=int,
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default=2,
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help="Number of errors allowed for matching primers [default = 2]")
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class Primer:
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collection={}
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def __init__(self, sequence, taglength, direct=True, error=2, verbose=False):
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'''
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@param sequence:
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@type sequence:
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@param direct:
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@type direct:
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'''
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assert sequence not in Primer.collection \
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or Primer.collection[sequence]==taglength, \
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"Primer %s must always be used with tags of the same length" % sequence
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Primer.collection[sequence]=taglength
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self.raw=sequence
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self.sequence = Nuc_Seq(b"primer", sequence)
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self.lseq = len(self.sequence)
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self.align=FreeEndGapFullMatch()
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self.align.match=4
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self.align.mismatch=-2
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self.align.opengap=-2
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self.align.extgap=-2
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self.error=error
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self.minscore = (self.lseq-error) * self.align.match + error * self.align.mismatch
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self.taglength=taglength
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self.align.seqB=self.sequence
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self.direct = direct
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self.verbose=verbose
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def reverse_complement(self):
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p = Primer(self.raw,
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self.taglength,
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not self.direct,verbose=self.verbose,
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error=self.error)
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p.sequence=p.sequence.reverse_complement
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p.align.seqB=p.sequence
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return p
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def __hash__(self):
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return hash(str(self.raw))
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def __eq__(self,primer):
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return self.raw==primer.raw
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def __call__(self,sequence):
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if len(sequence) <= self.lseq:
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return None
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self.align.seqA=sequence
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ali=self.align()
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if ali.score >= self.minscore:
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score = ali.score
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start = ali[1].gaps[0][1]
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end = len(ali[1])-ali[1].gaps[-1][1]
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if self.taglength is not None:
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if self.sequence.revcomp:
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if (len(sequence)-end) >= self.taglength:
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tag = sequence.clone()
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tag = tag[end:end+self.taglength]
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tag = tag.reverse_complement.seq
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else:
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tag=None
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else:
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if start >= self.taglength:
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tag = sequence.clone()
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tag = tag[start - self.taglength:start].seq
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else:
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tag=None
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else:
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tag=None
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return score,start,end,tag
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return None
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def __str__(self):
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return "%s: %s" % ({True:'D',False:'R'}[self.direct],self.raw)
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__repr__=__str__
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cdef dict read_info_view(info_view, error=2, verbose=False):
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infos = {}
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for p in info_view:
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forward=Primer(p[b'forward_primer'],
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len(p[b'forward_tag']) if p[b'forward_tag']!=b'-' else None,
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True,
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error=error,verbose=verbose)
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fp = infos.get(forward,{})
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infos[forward]=fp
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reverse=Primer(p[b'reverse_primer'],
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len(p[b'reverse_tag']) if p[b'reverse_tag']!=b'-' else None,
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False,
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error=error,verbose=verbose)
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rp = infos.get(reverse,{})
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infos[reverse]=rp
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cf=forward.reverse_complement()
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cr=reverse.reverse_complement()
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dpp=fp.get(cr,{})
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fp[cr]=dpp
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rpp=rp.get(cf,{})
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rp[cf]=rpp
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tags = (p[b'forward_tag'] if p[b'forward_tag']!=b'-' else None,
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p[b'reverse_tag'] if p[b'reverse_tag']!=b'-' else None)
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assert tags not in dpp, \
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"Tag pair %s is already used with primer pairs: (%s,%s)" % (str(tags),forward,reverse)
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# Save additional data
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special_keys = [b'forward_primer', b'reverse_primer', b'forward_tag', b'reverse_tag']
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data={}
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for key in p:
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if key not in special_keys:
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data[key] = p[key]
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dpp[tags] = data
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rpp[tags] = data
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return infos
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cdef tuple annotate(sequence, infos, verbose=False):
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def sortMatch(m1, m2):
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if m1[1] is None and m2[1] is None:
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return 0
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if m1[1] is None:
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return 1
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if m2[1] is None:
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return -1
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return (m1[1][1] > m2[1][2]) - (m1[1][1] < m2[1][2])
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if hasattr(sequence, "quality_array"):
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q = -reduce(lambda x,y:x+y,(math.log10(z) for z in sequence.quality_array),0)/len(sequence.quality_array)*10
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sequence[b'avg_quality']=q
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q = -reduce(lambda x,y:x+y,(math.log10(z) for z in sequence.quality_array[0:10]),0)
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sequence[b'head_quality']=q
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if len(sequence.quality_array[10:-10]) :
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q = -reduce(lambda x,y:x+y,(math.log10(z) for z in sequence.quality_array[10:-10]),0)/len(sequence.quality_array[10:-10])*10
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sequence[b'mid_quality']=q
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q = -reduce(lambda x,y:x+y,(math.log10(z) for z in sequence.quality_array[-10:]),0)
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sequence[b'tail_quality']=q
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directmatch = [(p,p(sequence)) for p in infos]
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directmatch.sort(key=cmp_to_key(sortMatch))
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directmatch=directmatch[0] if directmatch[0][1] is not None else None
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if directmatch is None:
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sequence[b'error']=b'No primer match'
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return False,sequence
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match = sequence[directmatch[1][1]:directmatch[1][2]]
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sequence[b'seq_length_ori']=len(sequence)
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sequence = sequence[directmatch[1][2]:]
|
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if directmatch[0].direct:
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sequence[b'direction']=b'forward'
|
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sequence[b'forward_score']=directmatch[1][0]
|
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sequence[b'forward_primer']=directmatch[0].raw
|
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sequence[b'forward_match']=match.seq
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|
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else:
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sequence[b'direction']=b'reverse'
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sequence[b'reverse_score']=directmatch[1][0]
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sequence[b'reverse_primer']=directmatch[0].raw
|
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sequence[b'reverse_match']=match.seq
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||||
|
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infos = infos[directmatch[0]]
|
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reversematch = [(p,p(sequence)) for p in infos if p is not None]
|
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reversematch.sort(key=cmp_to_key(sortMatch))
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reversematch = reversematch[0] if reversematch[0][1] is not None else None
|
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|
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if reversematch is None and None not in infos:
|
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if directmatch[0].direct:
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message = b'No reverse primer match'
|
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else:
|
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message = b'No direct primer match'
|
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|
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sequence[b'error']=message
|
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return False,sequence
|
||||
|
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if reversematch is None:
|
||||
sequence[b'status']=b'partial'
|
||||
|
||||
if directmatch[0].direct:
|
||||
tags=(directmatch[1][3],None)
|
||||
else:
|
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tags=(None,directmatch[1][3])
|
||||
|
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samples = infos[None]
|
||||
|
||||
else:
|
||||
sequence[b'status']=b'full'
|
||||
|
||||
match = sequence[reversematch[1][1]:reversematch[1][2]]
|
||||
match = match.reverse_complement
|
||||
sequence = sequence[0:reversematch[1][1]]
|
||||
|
||||
if directmatch[0].direct:
|
||||
tags=(directmatch[1][3],reversematch[1][3])
|
||||
sequence[b'reverse_score']=reversematch[1][0]
|
||||
sequence[b'reverse_primer']=reversematch[0].raw
|
||||
sequence[b'reverse_match']=match.seq
|
||||
|
||||
else:
|
||||
tags=(reversematch[1][3],directmatch[1][3])
|
||||
sequence[b'forward_score']=reversematch[1][0]
|
||||
sequence[b'forward_primer']=reversematch[0].raw
|
||||
sequence[b'forward_match']=match.seq
|
||||
|
||||
if tags[0] is not None:
|
||||
sequence[b'forward_tag'] = tags[0]
|
||||
if tags[1] is not None:
|
||||
sequence[b'reverse_tag'] = tags[1]
|
||||
|
||||
samples = infos[reversematch[0]]
|
||||
|
||||
if not directmatch[0].direct:
|
||||
sequence=sequence.reverse_complement
|
||||
|
||||
sample=None
|
||||
|
||||
if tags[0] is not None: # Direct tag known
|
||||
if tags[1] is not None: # Reverse tag known
|
||||
sample = samples.get(tags, None)
|
||||
else: # Reverse tag known
|
||||
s=[samples[x] for x in samples if x[0]==tags[0]]
|
||||
if len(s)==1:
|
||||
sample=s[0]
|
||||
elif len(s)>1:
|
||||
sequence[b'error']=b'multiple samples match tags'
|
||||
return False,sequence
|
||||
else:
|
||||
sample=None
|
||||
else:
|
||||
if tags[1] is not None: # Reverse tag known
|
||||
s=[samples[x] for x in samples if x[1]==tags[1]]
|
||||
if len(s)==1:
|
||||
sample=s[0]
|
||||
elif len(s)>1:
|
||||
sequence[b'error']=b'multiple samples match tags'
|
||||
return False,sequence
|
||||
else: # Reverse tag known
|
||||
sample=None
|
||||
|
||||
if sample is None:
|
||||
sequence[b'error']=b"Cannot assign sequence to a sample"
|
||||
return False,sequence
|
||||
|
||||
sequence.update(sample)
|
||||
sequence[b'seq_length']=len(sequence)
|
||||
|
||||
return True, sequence
|
||||
|
||||
|
||||
def run(config):
|
||||
|
||||
DMS.obi_atexit()
|
||||
|
||||
logger("info", "obi ngsfilter")
|
||||
|
||||
assert config['ngsfilter']['info_view'] is not None, "Option -t must be specified"
|
||||
|
||||
# Open the input
|
||||
input = open_uri(config['obi']['inputURI'])
|
||||
if input is None:
|
||||
raise Exception("Could not read input view")
|
||||
if input[2] != View_NUC_SEQS:
|
||||
raise NotImplementedError('obi ngsfilter only works on NUC_SEQS views')
|
||||
|
||||
# Open the output
|
||||
output = open_uri(config['obi']['outputURI'],
|
||||
input=False,
|
||||
newviewtype=View_NUC_SEQS)
|
||||
|
||||
if output is None:
|
||||
raise Exception("Could not create output view")
|
||||
|
||||
entries = input[1]
|
||||
o_view = output[1]
|
||||
|
||||
# Open the the view containing the informations about the tags and the primers
|
||||
info_input = open_uri(config['ngsfilter']['info_view'])
|
||||
if info_input is None:
|
||||
raise Exception("Could not read the view containing the informations about the tags and the primers")
|
||||
info_view = info_input[1]
|
||||
|
||||
# Open the unidentified view
|
||||
if config['ngsfilter']['unidentified'] is not None:
|
||||
unidentified_input = open_uri(config['ngsfilter']['unidentified'],
|
||||
input=False,
|
||||
newviewtype=View_NUC_SEQS)
|
||||
if unidentified_input is None:
|
||||
raise Exception("Could not open the view containing the unidentified reads")
|
||||
unidentified = unidentified_input[1]
|
||||
|
||||
# Initialize the progress bar
|
||||
pb = ProgressBar(len(entries), config, seconde=5)
|
||||
|
||||
# Check and store primers and tags
|
||||
infos = read_info_view(info_view, error=config['ngsfilter']['error'])
|
||||
|
||||
g = 0
|
||||
u = 0
|
||||
i = 0
|
||||
try:
|
||||
for iseq in entries:
|
||||
pb(i)
|
||||
i+=1
|
||||
modseq = Nuc_Seq.new_from_stored(iseq)
|
||||
good, oseq = annotate(modseq, infos)
|
||||
if good:
|
||||
o_view[g].set(oseq.id, oseq.seq, definition=oseq.definition, quality=oseq.quality, tags=oseq)
|
||||
g+=1
|
||||
elif unidentified is not None:
|
||||
unidentified[u].set(oseq.id, oseq.seq, definition=oseq.definition, quality=oseq.quality, tags=oseq)
|
||||
u+=1
|
||||
except Exception, e:
|
||||
raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
|
||||
|
||||
input[0].close()
|
||||
output[0].close()
|
||||
info_input[0].close()
|
||||
unidentified_input[0].close()
|
||||
|
||||
|
||||
|
||||
# TODO ??
|
||||
# if options.taglist is not None:
|
||||
#TODO: Patch when no taglists
|
||||
# else:
|
||||
# options.direct=options.direct.lower()
|
||||
# options.reverse=options.reverse.lower()
|
||||
# primers={options.direct:(options.taglength,{})}
|
||||
# if options.reverse is not None:
|
||||
# reverse = options.reverse
|
||||
# else:
|
||||
# reverse = '-'
|
||||
# primers[options.direct][1][reverse]={'-':('-','-',True,None)}
|
||||
|
||||
Reference in New Issue
Block a user