def convertMali2Alignlib(mali):
"""convert a multiple alignment into an alignlib multiple alignment object."""
import alignlib
m = alignlib.makeMultipleAlignment()
for identifier in mali.getIdentifiers():
a = alignlib.makeAlignatumFromString(mali[identifier])
m.add(a)
return m
def convertMali2Alignlib( mali ):
"""convert a multiple alignment into an alignlib multiple alignment object."""
import alignlib
m = alignlib.makeMultipleAlignment()
for identifier in mali.getIdentifiers():
a = alignlib.makeAlignatumFromString( mali[identifier] )
m.add( a )
return m
def convertMali2Mali( mali ):
"""convert a mali to a profile."""
new_mali = alignlib.makeMultipleAlignment()
for id in mali.getIdentifiers():
s = alignlib.makeAlignatumFromString( mali[id] )
s.thisown = 0
new_mali.addAlignatum( s )
return new_mali
def convertMali2Alignlib( mali ):
'''convert a multiple alignment of type :class:`Mali`
into an alignlib multiple alignment object.
'''
import alignlib
m = alignlib.makeMultipleAlignment()
for identifier in mali.getIdentifiers():
a = alignlib.makeAlignatum( mali[identifier] )
m.add( a )
return m
def applyMethod(self, neighbours):
"""apply the method."""
# build multiple alignment
mali = alignlib.makeMultipleAlignment()
query_nid = neighbours.mQueryToken
sequence = self.mFasta.getSequence(query_nid)
mali.add(alignlib.makeAlignatum(sequence))
qseq = alignlib.makeSequence(sequence)
alignator = alignlib.makeAlignatorDPFull(alignlib.ALIGNMENT_GLOBAL,
-10.0, -1.0, True, True, True,
True)
for n in neighbours.mMatches:
if n.mSbjctToken == query_nid: continue
sequence = self.mFasta.getSequence(n.mSbjctToken)
blast_query2sbjct = n.getAlignment()
if blast_query2sbjct == None:
raise ValueError(
"AddaRealignment.py needs a reference alignment.")
realign_query2sbjct = alignlib.makeAlignmentVector()
sseq = alignlib.makeSequence(sequence)
qseq.useSegment(n.mQueryFrom, n.mQueryTo)
sseq.useSegment(n.mSbjctFrom, n.mSbjctTo)
realign_query2sbjct = alignlib.makeAlignmentVector()
alignator.align(realign_query2sbjct, qseq, sseq)
nidentical = alignlib.getAlignmentIdentity(realign_query2sbjct,
blast_query2sbjct,
alignlib.RR)
nblast = blast_query2sbjct.getNumAligned()
nrealigned = realign_query2sbjct.getNumAligned()
self.mOutfile.write( "%s\t%s\t%i\t%i\t%i\n" % \
(n.mQueryToken, n.mSbjctToken, nidentical, nblast, nrealigned ) )
if nidentical == nblast:
self.mNIdentical += 1
else:
self.mNDifferent += 1
def readPicasso( infile ):
"""read alignment in the non-defined picasso format.
"""
mali = alignlib.makeMultipleAlignment()
while 1:
line = infile.readline()
if not line: break
x = re.search( "\d+\s+([A-Z\-\.]*)\s+\d+", line)
if x:
s = x.groups()[0]
a = alignlib.makeAlignatumFromString(s)
a.thisown = 0
mali.addAlignatum( a )
return mali
def applyMethod(self, neighbours ):
"""apply the method."""
# build multiple alignment
mali = alignlib.makeMultipleAlignment()
query_nid = neighbours.mQueryToken
sequence = self.mFasta.getSequence( query_nid )
mali.add( alignlib.makeAlignatum( sequence ) )
qseq = alignlib.makeSequence( sequence )
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_GLOBAL,
-10.0, -1.0, True, True, True, True)
for n in neighbours.mMatches:
if n.mSbjctToken == query_nid: continue
sequence = self.mFasta.getSequence( n.mSbjctToken )
blast_query2sbjct = n.getAlignment()
if blast_query2sbjct == None:
raise ValueError( "AddaRealignment.py needs a reference alignment.")
realign_query2sbjct = alignlib.makeAlignmentVector()
sseq = alignlib.makeSequence( sequence )
qseq.useSegment( n.mQueryFrom, n.mQueryTo )
sseq.useSegment( n.mSbjctFrom, n.mSbjctTo )
realign_query2sbjct = alignlib.makeAlignmentVector()
alignator.align( realign_query2sbjct, qseq, sseq )
nidentical = alignlib.getAlignmentIdentity( realign_query2sbjct, blast_query2sbjct, alignlib.RR )
nblast = blast_query2sbjct.getNumAligned()
nrealigned = realign_query2sbjct.getNumAligned()
self.mOutfile.write( "%s\t%s\t%i\t%i\t%i\n" % \
(n.mQueryToken, n.mSbjctToken, nidentical, nblast, nrealigned ) )
if nidentical == nblast:
self.mNIdentical += 1
else:
self.mNDifferent += 1
def buildMali(self, query_nid, neighbours):
"""build a multiple alignment from a set of neighbours.
"""
# build multiple alignment
mali = alignlib.makeMultipleAlignment()
query_sequence = self.mFasta.getSequence(query_nid)
mali.add(alignlib.makeAlignatum(query_sequence))
qseq = alignlib.makeSequence(query_sequence)
alignator = alignlib.makeAlignatorDPFull(alignlib.ALIGNMENT_LOCAL, -10,
-2)
nskipped = 0
for n in neighbours[:self.mMaxNumNeighbours]:
if n.mSbjctToken == query_nid: continue
if n.mEvalue > self.mMaxEvalue:
nskipped += 1
continue
sequence = self.mFasta.getSequence(n.mSbjctToken)
E.debug("adding %s" % str(n))
map_query2sbjct = n.getAlignment()
if map_query2sbjct == None:
sseq = alignlib.makeSequence(sequence)
qseq.useSegment(n.mQueryFrom, n.mQueryTo)
sseq.useSegment(n.mSbjctFrom, n.mSbjctTo)
map_query2sbjct = alignlib.makeAlignmentVector()
alignator.align(map_query2sbjct, qseq, sseq)
if map_query2sbjct.getLength() == 0:
self.warn("empty alignment: %s" % str(n))
nskipped += 1
continue
if map_query2sbjct.getRowTo() > len(query_sequence):
self.warn( "alignment out of bounds for query: %i>%i, line=%s" %\
(map_query2sbjct.getRowTo(), len(query_sequence), str(n)))
nskipped += 1
continue
elif map_query2sbjct.getColTo() > len(sequence):
self.warn( "alignment out of bounds for sbjct: %i>%i, line=%s" %\
(map_query2sbjct.getColTo(), len(sequence), str(n)))
nskipped += 1
continue
try:
mali.add(alignlib.makeAlignatum(sequence),
map_query2sbjct,
mali_is_in_row=True,
insert_gaps_mali=False,
insert_gaps_alignatum=True,
use_end_mali=True,
use_end_alignatum=False)
except RuntimeError, msg:
self.warn("problem when building alignment for %s: msg=%s" %
(str(n), msg))
nskipped += 1
continue
lines = map(lambda x: string.split(x[:-1], "\t"), open(a, "r").readlines())
param_sequences = {}
for token, sequence in lines:
if param_sequences.has_key(token):
if len(param_sequences[token]) >= len(sequence):
continue
param_sequences[token] = sequence
tbl_nrdb = Table_nrdb( dbhandle )
query_sequence = None
if param_unaligned:
mali = alignlib.makeMultipleAlignmentDots(param_compression)
else:
mali = alignlib.makeMultipleAlignment()
map_query2sbjct = alignlib.makeAlignataVector()
lines = map( lambda x: string.split( x[:-1], "\t")[:9], filter( lambda x: x[0] != "#", sys.stdin.readlines()))
if param_sort_order:
data = []
for line in lines:
sbjct_nid = line[1]
if param_sort_order.has_key( sbjct_nid ):
o = param_sort_order[sbjct_nid]
else:
o = len(param_sort_order)
data.append( (o, line) )
def buildMali(self, query_nid, neighbours ):
"""build a multiple alignment from a set of neighbours.
"""
# build multiple alignment
mali = alignlib.makeMultipleAlignment()
query_sequence = self.mFasta.getSequence( query_nid )
mali.add( alignlib.makeAlignatum( query_sequence ) )
qseq = alignlib.makeSequence( query_sequence )
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL,
-10, -2)
nskipped = 0
for n in neighbours[:self.mMaxNumNeighbours]:
if n.mSbjctToken == query_nid: continue
if n.mEvalue > self.mMaxEvalue:
nskipped += 1
continue
sequence = self.mFasta.getSequence( n.mSbjctToken )
E.debug( "adding %s" % str(n) )
map_query2sbjct = n.getAlignment()
if map_query2sbjct == None:
sseq = alignlib.makeSequence( sequence )
qseq.useSegment( n.mQueryFrom, n.mQueryTo )
sseq.useSegment( n.mSbjctFrom, n.mSbjctTo )
map_query2sbjct = alignlib.makeAlignmentVector()
alignator.align( map_query2sbjct, qseq, sseq )
if map_query2sbjct.getLength() == 0:
self.warn( "empty alignment: %s" % str( n ) )
nskipped += 1
continue
if map_query2sbjct.getRowTo() > len(query_sequence):
self.warn( "alignment out of bounds for query: %i>%i, line=%s" %\
(map_query2sbjct.getRowTo(), len(query_sequence), str(n)))
nskipped += 1
continue
elif map_query2sbjct.getColTo() > len(sequence):
self.warn( "alignment out of bounds for sbjct: %i>%i, line=%s" %\
(map_query2sbjct.getColTo(), len(sequence), str(n)))
nskipped += 1
continue
try:
mali.add( alignlib.makeAlignatum( sequence ),
map_query2sbjct,
mali_is_in_row = True,
insert_gaps_mali = False,
insert_gaps_alignatum = True,
use_end_mali = True,
use_end_alignatum = False )
except RuntimeError, msg:
self.warn( "problem when building alignment for %s: msg=%s" % (str(n), msg))
nskipped += 1
continue