def PrintAlignedSequences( sequence1, sequence2, chain = None, format="modeller" ):
## align sequences by identity
seq_row = alignlib.makeSequence( sequence1 )
seq_col = alignlib.makeSequence( sequence2 )
alignator = alignlib.makeAlignatorFullDP( -0.0, -0.0 )
map_row2col = alignlib.makeAlignataVector()
alignator.Align( seq_row, seq_col, map_row2col )
lines = string.split(alignlib.writePairAlignment( seq_row, seq_col, map_row2col ), "\n")
if format == "modeller":
first_res, sequence, last_res = string.split( lines[0], "\t" )
print ">P1;structure"
print "structureX: %s : %s : %s : %s : %s : : : : " % ("structure", first_res, "" , last_res, "" )
print "%s*" % sequence
first_res, sequence, last_res = string.split( lines[1], "\t" )
print ">P1;sequence"
print "sequence:%s : %s : %s : %s : %s : : : : " % ("sequence" , first_res, "", last_res, "")
print "%s*" % sequence
else:
print lines
def GetAlignmentBetweenCorrespondingAtoms( coordinates1, coordinates2, cutoff ):
"""returns a list of atom positions, which are close to each other.
This is done via a dynamic programming step. First all versus all comparison
between atom positions is done. Only those positions are kept below cutoff.
"""
dots = alignlib.makeAlignataMatrixRow()
for i in range(len(coordinates1)):
x1,y1,z1 = coordinates1[i]
for j in range(len(coordinates2)):
x2,y2,z2 = coordinates2[j]
d = math.sqrt( (x1-x2)*(x1-x2) + (y1-y2)*(y1-y2) + (z1-z2)*(z1-z2))
if d <= cutoff:
dots.addPairExplicit(i+1, j+1, 1)
seq1 = alignlib.makeSequence ("A" * len(coordinates1))
seq2 = alignlib.makeSequence ("A" * len(coordinates2))
if dots.getLength() <= 3:
return None
dottor = alignlib.makeAlignatorDummy( dots )
alignator = alignlib.makeAlignatorDotsSquared( 0, 0, dottor)
map_a2b = alignlib.makeAlignataVector()
alignator.Align( seq1, seq2, map_a2b)
return map_a2b
def CheckAlignments( peptide_sequences, query_token, other_tokens ):
"""check wether query aligns to all others.
"""
if param_loglevel >= 3:
print "# checking query %s and sbjcts %s" % (query_token, str(other_tokens))
sys.stdout.flush()
if query_token not in peptide_sequences:
return True
result = alignlib.makeAlignmentVector()
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL,
-10.0, -1.0 )
row_seq = alignlib.makeSequence(peptide_sequences[query_token])
for x in other_tokens:
if x not in peptide_sequences:
continue
col_seq = alignlib.makeSequence( peptide_sequences[x] )
alignator.align( result, row_seq, col_seq )
if param_loglevel >= 5:
print "# %s - %s = %f" % (query_token, x, result.getScore())
if result.getScore() > param_min_alignment_score:
return True
return False
def PrintAlignedSequences(sequence1, sequence2, chain=None, format="modeller"):
## align sequences by identity
seq_row = alignlib.makeSequence(sequence1)
seq_col = alignlib.makeSequence(sequence2)
alignator = alignlib.makeAlignatorFullDP(-0.0, -0.0)
map_row2col = alignlib.makeAlignataVector()
alignator.Align(seq_row, seq_col, map_row2col)
lines = string.split(
alignlib.writePairAlignment(seq_row, seq_col, map_row2col), "\n")
if format == "modeller":
first_res, sequence, last_res = string.split(lines[0], "\t")
print ">P1;structure"
print "structureX: %s : %s : %s : %s : %s : : : : " % (
"structure", first_res, "", last_res, "")
print "%s*" % sequence
first_res, sequence, last_res = string.split(lines[1], "\t")
print ">P1;sequence"
print "sequence:%s : %s : %s : %s : %s : : : : " % (
"sequence", first_res, "", last_res, "")
print "%s*" % sequence
else:
print lines
def getMapPeptide2Cds( peptide_sequence, cds_sequence, options ):
"""get map between peptide sequence and cds sequence.
The returned alignment is in nucleotides.
"""
## remove whitespaces form protein sequence
p = re.sub(" ", "", peptide_sequence )
## remove gaps and whitespaces from cds
c = re.sub("[ .-]", "", cds_sequence )
w = Genomics.Protein2Wobble( p.upper() )
if options.loglevel >= 6:
options.stdlog.write( "# peptide original (%5i): %s\n" % (len(p), p) )
options.stdlog.write( "# cds original (%5i): %s\n" % (len(c), c) )
options.stdlog.write( "# wobble sequence (%5i): %s\n" % (len(w), w) )
options.stdlog.flush()
seq_wobble = alignlib.makeSequence( w )
seq_cds = alignlib.makeSequence( string.upper(c) )
seq_peptide = alignlib.makeSequence( p )
map_p2c = alignlib.makeAlignmentVector()
try:
AlignCodonBased( seq_wobble, seq_cds, seq_peptide, map_p2c, options = options )
except ValueError, msg:
raise ValueError( "mapping error for sequence: %s" % (msg) )
def AlignPair( pair, anchor = 0 ):
"""align a pair of introns."""
map_intron_a2b = alignlib.makeAlignmentVector()
if param_loglevel >= 1:
print "# aligning %s-%i with %s-%i: lengths %i and %i" % (pair.mToken1, pair.mIntronId1,
pair.mToken2, pair.mIntronId2,
len(pair.mAlignedSequence1),
len(pair.mAlignedSequence2))
sys.stdout.flush()
s1 = "A" * anchor + pair.mAlignedSequence1 + "A" * anchor
s2 = "A" * anchor + pair.mAlignedSequence2 + "A" * anchor
if param_method == "dialigned":
dialign.Align( s1, s2, map_intron_a2b )
elif param_method == "dialignedlgs":
dialignlgs.Align( s1, s2, map_intron_a2b )
elif param_method == "dbaligned":
dba.Align( s1, s2, map_intron_a2b )
elif param_method == "clusaligned":
raise NotImplementedError("clustalw wrapper not up-to-date")
clustal.Align( s1, s2, map_intron_a2b )
if anchor:
map_intron_a2b.removeRowRegion( anchor + len(pair.mAlignedSequence1) + 1, map_intron_a2b.getRowTo() )
map_intron_a2b.removeRowRegion( 1, anchor)
map_intron_a2b.removeColRegion( anchor + len(pair.mAlignedSequence2) + 1, map_intron_a2b.getColTo() )
map_intron_a2b.removeColRegion( 1, anchor)
map_intron_a2b.moveAlignment( -anchor, -anchor )
if map_intron_a2b.getLength() == 0:
if param_loglevel >= 1:
print "# Error: empty intron alignment"
return False
seq1 = alignlib.makeSequence( pair.mAlignedSequence1 )
seq2 = alignlib.makeSequence( pair.mAlignedSequence2 )
data = alignlib.AlignmentFormatExplicit( map_intron_a2b, seq1, seq2 )
pair.mFrom1, pair.mAlignedSequence1, pair.mTo1 = data.mRowFrom, data.mRowAlignment, data.mRowTo
pair.mFrom2, pair.mAlignedSequence2, pair.mTo2 = data.mColFrom, data.mColAlignment, data.mColTo
pair.mMethod = param_method
pair.mNumGaps, pair.mLength = map_intron_a2b.getNumGaps(), map_intron_a2b.getLength()
pair.mAligned = pair.mLength - pair.mNumGaps
if param_loglevel >= 2:
print "# alignment success", pair.mAlignedSequence1, pair.mAlignedSequence2
return True
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 _buildProfile(nid, start, end):
neighbours = index.getNeighbours(nid)
mali = align.buildMali(nid, neighbours)
prof = alignlib.makeProfile(mali)
E.info("nid: %i, neighours=%i" % (nid, len(neighbours)))
prof.useSegment(start, end)
prof.prepare()
seq = fasta.getSequence(nid)
return alignlib.makeSequence(seq), prof
def _buildProfile(nid, start, end):
neighbours = index.getNeighbours(nid)
mali = align.buildMali(nid, neighbours)
prof = alignlib.makeProfile(mali)
E.info("nid: %i, neighours=%i" % (nid, len(neighbours)))
prof.useSegment(start, end)
prof.prepare()
seq = fasta.getSequence(nid)
return alignlib.makeSequence(seq), prof
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 CreateAlignandumObjects( self, sources ):
tbl_nrdb = Table_nrdb( self.dbhandle )
alignanda = []
for id, nid, nid_from, nid_to in sources:
if self.mLogLevel >= 2:
print id,
sys.stdout.flush()
sequence = tbl_nrdb.Get_Sequence_From_NID( nid )
alignandum = alignlib.makeSequence( sequence[nid_from-1:nid_to] )
alignanda.append( (id, alignandum) )
if self.mLogLevel >= 2:
print
return alignanda
def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser( version = "%prog version: $Id: gpipe/prediction2pairs.py 2031 2008-07-15 09:19:05Z andreas $", usage = globals()["__doc__"])
parser.add_option( "-g", "--genome-file", dest="genome_file", type="string",
help="filename with genomic data (indexed)." )
parser.add_option( "-c", "--cds", dest="filename_cds", type="string",
help="filename with cds seguences." )
parser.add_option( "-f", "--format", dest="format", type="choice",
choices=("paired_fasta", ),
help="output format, valid options are: paired_fasta: concatenated pairwise alignments in FASTA format" )
parser.set_defaults(
genome_file = "genome",
filename_cds = "cds.fasta",
format = "paired_fasta",
filename_suffix = ".fasta",
filename_prefix = "",
)
(options, args) = E.Start( parser, add_psql_options = True )
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(1)
fasta = IndexedFasta.IndexedFasta( options.genome_file )
## reading CDS sequences
if options.filename_cds:
cds_sequences = Genomics.ReadPeptideSequences( open(options.filename_cds, "r") )
else:
cds_sequences = {}
if options.loglevel >= 1:
options.stdlog.write( "# read %i CDS sequences\n" % len(cds_sequences) )
last_filename_genome = None
p = PredictionParser.PredictionParserEntry()
ninput, noutput, nsanity, n3, nlength = 0, 0, 0, 0, 0
for line in options.stdin:
if line[0] == "#": continue
if line[0] == '"': continue
p.Read(line)
ninput += 1
genomic_fragment = fasta.getSequence( p.mSbjctToken, p.mSbjctStrand,
p.mSbjctGenomeFrom, p.mSbjctGenomeTo )
if len(genomic_fragment) == 0:
raise "ERROR: empty fragment %s:%s for line" % (p.mSbjctGenomeFrom, p.mSbjctGenomeTo), line
try:
cds_fragment = cds_sequences[p.mQueryToken]
except KeyError:
options.stdlog.write( "# ERROR: cds not found: query %s.\n" % p.mQueryToken )
continue
map_query2sbjct, genomic_fragment = Genomics.Alignment2CDNA( p.mMapPeptide2Genome,
query_from = p.mQueryFrom,
sbjct_from = 0,
genome = genomic_fragment )
## check for errors:
if map_query2sbjct.getRowTo() != p.mQueryTo * 3:
options.stdlog.write( "# ERROR: boundary shift in query at line %s\n# %i %i\n" % (line, map_query2sbjct.getRowTo(), p.mQueryTo * 3 ) )
if map_query2sbjct.getColTo() > len(genomic_fragment):
options.stdlog.write( "# ERROR: length mismatch in line %s\n# genomic fragment (%i) shorter than last aligned residue (%i)\n" %\
(line, len(genomic_fragment), map_query2sbjct.getColTo()) )
options.stdlog.write( "# cds %s\n# genomic %s\n" % (str( cds_fragment ), genomic_fragment ))
nlength += 1
continue
if map_query2sbjct.getRowTo() > len(cds_fragment):
options.stdlog.write( "# ERROR: length mismatch in line %s\n# cds fragment (%i) shorter than last aligned residue (%i)\n" %\
(line, len(cds_fragment), map_query2sbjct.getRowTo()) )
options.stdlog.write( "# cds %s\n# genomic %s\n" % (str( cds_fragment ), genomic_fragment ))
nlength += 1
continue
cds_seq = alignlib.makeSequence( cds_fragment )
genomic_seq = alignlib.makeSequence( genomic_fragment )
f = alignlib.AlignmentFormatExplicit( map_query2sbjct, cds_seq, genomic_seq )
row_ali = f.mRowAlignment
col_ali = f.mColAlignment
row_ali, col_ali = Genomics.RemoveFrameShiftsFromAlignment(row_ali, col_ali)
row_ali = Genomics.MaskStopCodons( row_ali )
col_ali = Genomics.MaskStopCodons( col_ali )
if len(row_ali) != len(col_ali):
options.stdlog.write( "# ERROR: wrong alignment lengths.\n" )
sys.exit(1)
if len(row_ali) % 3 or len(col_ali) % 3:
options.stdlog.write( "# ERROR: sequences are not a multiple of 3 in line: %s\n" % line )
options.stdlog.write( "# %6i %s\n# %6i %s\n" % (len(row_ali), str(row_ali), len(col_ali), str(col_ali) ) )
n3 += 1
input = re.sub( "[-X]", "", p.mTranslation )
ref = re.sub( "[-X]", "", Genomics.TranslateDNA2Protein( col_ali ) )
if input != ref:
if options.loglevel >= 1:
options.stdlog.write("# sanity check failed for %s - %s\n# %6i %s\n# %6i %s\n" % (p.mPredictionId, p.mQueryToken,
len(input), input,
len(ref), ref ) )
nsanity += 1
continue
options.stdout.write( ">%s\n%s\n" % (p.mPredictionId, row_ali) )
options.stdout.write( ">%s_vs_%s_%s_%i_%i\n%s\n" % \
(p.mQueryToken, p.mSbjctToken, p.mSbjctStrand, p.mSbjctGenomeFrom, p.mSbjctGenomeTo, col_ali) )
noutput += 1
if options.loglevel >= 1:
options.stdlog.write("# ninput=%i, noutput=%i, nsanity=%i, nlength=%i, n3=%i\n" % (ninput, noutput, nsanity, nlength, n3) )
E.Stop()
def Align( self, method, anchor = 0, loglevel = 1 ):
"""align a pair of sequences.
get rid of this and use a method class instead in the future
"""
map_a2b = alignlib.makeAlignmentVector()
s1 = "A" * anchor + self.mSequence1 + "A" * anchor
s2 = "A" * anchor + self.mSequence2 + "A" * anchor
self.strand = "+"
if method == "dialign":
dialign = WrapperDialign.Dialign( self.mOptionsDialign )
dialign.Align( s1, s2, map_a2b )
elif method == "blastz":
blastz = WrapperBlastZ.BlastZ( self.mOptionsBlastZ )
blastz.Align( s1, s2, map_a2b )
if blastz.isReverseComplement():
self.strand = "-"
self.mSequence2 = Genomics.complement( self.mSequence2 )
elif method == "dialignlgs":
dialignlgs = WrapperDialign.Dialign( self.mOptionsDialignLGS )
dialignlgs.Align( s1, s2, map_a2b )
elif method == "dba":
dba = WrapperDBA.DBA()
dba.Align( s1, s2, map_a2b )
elif method == "clustal":
raise NotImplementedError( "clustal wrapper needs to be updated")
clustal = WrapperClustal.Clustal()
clustal.Align( s1, s2, map_a2b )
elif method == "nw":
seq1 = alignlib.makeSequence( s1 )
seq2 = alignlib.makeSequence( s2 )
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_GLOBAL,
gop=-12.0,
gep=-2.0 )
alignator.align( map_a2b, seq1, seq2 )
elif method == "sw":
seq1 = alignlib.makeSequence( s1 )
seq2 = alignlib.makeSequence( s2 )
alignlib.performIterativeAlignment( map_a2b, seq1, seq2, alignator_sw, min_score_sw )
else:
## use callback function
method(s1, s2, map_a2b)
if map_a2b.getLength() == 0:
raise AlignmentError("empty alignment")
if anchor:
map_a2b.removeRowRegion( anchor + len(self.mSequence1) + 1, map_a2b.getRowTo() )
map_a2b.removeRowRegion( 1, anchor)
map_a2b.removeColRegion( anchor + len(self.mSequence2) + 1, map_a2b.getColTo() )
map_a2b.removeColRegion( 1, anchor)
map_a2b.moveAlignment( -anchor, -anchor )
f = alignlib.AlignmentFormatExplicit( map_a2b,
alignlib.makeSequence( self.mSequence1),
alignlib.makeSequence( self.mSequence2) )
self.mMethod = method
self.mAlignment = map_a2b
self.mAlignedSequence1, self.mAlignedSequence2 = f.mRowAlignment, f.mColAlignment
f = alignlib.AlignmentFormatEmissions( map_a2b )
self.mAlignment1, self.mAlignment2 = f.mRowAlignment, f.mColAlignment
self.mAlignmentFrom1 = map_a2b.getRowFrom()
self.mAlignmentTo1 = map_a2b.getRowTo()
self.mAlignmentFrom2 = map_a2b.getColFrom()
self.mAlignmentTo2 = map_a2b.getColTo()
self.mNumGaps, self.mLength = map_a2b.getNumGaps(), map_a2b.getLength()
self.mAligned = self.mLength - self.mNumGaps
self.SetPercentIdentity()
self.SetBlockSizes()
t = target_exons[tt]
if r.mGenomeTo < t.mGenomeFrom:
rr += 1
continue
elif t.mGenomeTo < r.mGenomeFrom:
tt += 1
continue
overlap += ( min(r.mGenomeTo, t.mGenomeTo) - max(r.mGenomeFrom, t.mGenomeFrom))
rr += 1
tt += 1
if overlap == 0:
continue
map_reference2target.clear()
row = alignlib.makeSequence(reference.mTranslation)
col = alignlib.makeSequence(target.mTranslation)
alignator.align( map_reference2target, row, col )
f = alignlib.AlignmentFormatEmissions( map_reference2target )
row_ali, col_ali = f.mRowAlignment, f.mColAlignment
pidentity = 100.0 * alignlib.calculatePercentIdentity( map_reference2target, row, col )
psimilarity = 100.0 * alignlib.calculatePercentSimilarity( map_reference2target )
union = max( reference.mSbjctGenomeTo, target.mSbjctGenomeTo) - \
min( reference.mSbjctGenomeFrom, target.mSbjctGenomeFrom )
inter = min( reference.mSbjctGenomeTo, target.mSbjctGenomeTo) - \
max( reference.mSbjctGenomeFrom, target.mSbjctGenomeFrom )
assignment_id += 1
def AlignCodonBased( seq_wobble, seq_cds, seq_peptide, map_p2c, options,
diag_width = 2, max_advance = 2 ):
"""advance in codons in seq_wobble and match to nucleotides in seq_cds.
Due to alinglib this is all in one-based coordinates.
Takes care of frameshifts.
"""
map_p2c.clear()
gop, gep = -1.0, -1.0
matrix = alignlib.makeSubstitutionMatrixBackTranslation( 1, -10, 1, alignlib.getDefaultEncoder() )
pep_seq = seq_peptide.asString()
cds_seq = seq_cds.asString()
wobble_seq = seq_wobble.asString()
lcds = seq_cds.getLength()
lwobble = seq_wobble.getLength()
y = 0
x = 0
last_start = None
while x < lwobble and y < lcds:
xr = seq_wobble.asResidue( x )
# skip over masked chars in wobble - these are gaps
if seq_wobble.asChar(x) == "X":
x += 1
continue
# skip over masked chars in wobble - these are from
# masked chars in the peptide sequence
# Note to self: do not see all implications of this change
# check later.
if seq_wobble.asChar(x) == "N":
x += 1
continue
# skip over gaps in wobble
if seq_wobble.asChar(x) == "-":
x += 1
continue
s = matrix.getValue( xr, seq_cds.asResidue(y) )
if options.loglevel >= 6:
if (x % 3 == 0):
c = seq_cds.asChar(y) + seq_cds.asChar(y+1) + seq_cds.asChar(y+2)
options.stdlog.write( "# c=%s, x=%i, y=%i, aa=%s target=%s\n" % (c, x, y,
Genomics.MapCodon2AA( c ),
pep_seq[int(x/3)]) )
options.stdlog.write( "# x=%i\twob=%s\ty=%i\tcds=%s\txr=%s\tcds=%i\tscore=%s\n" % \
(x, seq_wobble.asChar(x), y, seq_cds.asChar(y), xr, seq_cds.asResidue(y), str(s) ))
# deal with mismatches
if s <= 0:
tmp_map_p2c = alignlib.makeAlignmentVector()
## backtrack to previous three codons and align
## three codons for double frameshifts that span two codons and
## produce two X's and six WWWWWW.
## number of nucleotides to extend (should be multiple of 3)
## less than 12 caused failure for some peptides.
d = 15
# extend by amound dx
dx = (x % 3) + d
x_start = max(0, x - dx )
# map to ensure that no ambiguous residue mappings
# exist after re-alignment
y_start = max(0, map_p2c.mapRowToCol( x_start, alignlib.RIGHT ))
if (x_start, y_start) == last_start:
raise ValueError( "infinite loop detected" )
last_start = (x_start, y_start)
x_end = min(x_start + 2 * d, len(wobble_seq) )
y_end = min(y_start + 2 * d, len(cds_seq) )
wobble_fragment = alignlib.makeSequence(wobble_seq[x_start:x_end])
cds_fragment = alignlib.makeSequence(cds_seq[y_start:y_end])
AlignExhaustive( wobble_fragment, cds_fragment, "", tmp_map_p2c, options )
if options.loglevel >= 10:
options.stdlog.write("# fragmented alignment from %i-%i, %i-%i:\n%s\n" % (x_start, x_end,
y_start, y_end,
str(alignlib.AlignmentFormatExplicit( tmp_map_p2c,
wobble_fragment,
cds_fragment ))))
options.stdlog.flush()
## clear alignment
map_p2c.removeRowRegion( x_start, x_end )
ngap = 0
last_x, last_y = None, None
for xxx in range( tmp_map_p2c.getRowFrom(), tmp_map_p2c.getRowTo() ):
yyy = tmp_map_p2c.mapRowToCol(xxx)
if yyy >= 0:
x = xxx + x_start
y = yyy + y_start
xr = seq_wobble.asResidue(x)
s = matrix.getValue( seq_wobble.asResidue(x), seq_cds.asResidue(y) )
if s < 0:
raise ValueError("mismatched residue wobble: %i (%s), cds: %i (%s)" % (x, seq_wobble.asChar(x), y, seq_cds.asChar(y)))
map_p2c.addPair( x, y, s)
last_x, last_y = x, y
if options.loglevel >= 6:
options.stdlog.write( "# reset: x=%i\twob=%s\ty=%i\tcds=%s\txr=%s\tcds=%i\tscore=%i\n" % \
(x, seq_wobble.asChar(x), y, seq_cds.asChar(y), xr, seq_cds.asResidue(y), s ))
options.stdlog.flush()
ngap = 0
else:
ngap += 1
# treat special case of double frameshifts. They might cause a petide/wobble residue
# to be eliminated and thus the translated sequences will differ.
# simply delete the last residue between x and y and move to next codon.
if ngap == 3:
map_p2c.removeRowRegion( last_x, last_x + 1 )
last_x += 1
map_p2c.addPair( last_x, last_y )
if options.loglevel >= 6:
options.stdlog.write( "# double: x=%i\twob=%s\ty=%i\tcds=%s\txr=%s\tcds=%i\tscore=%i\n" % \
(last_x, seq_wobble.asChar(last_x), last_y, seq_cds.asChar(last_y), xr, seq_cds.asResidue(last_y), s ))
options.stdlog.flush()
ngap = 0
## exit condition if alignment is shorter than problematic residue
## need to catch this to avoid infinite loop.
if tmp_map_p2c.getRowTo() < d:
if lwobble - x <= 4:
## only last codon is missing, so ok
break
else:
raise ValueError("failure to align in designated window.")
s = 0
s = matrix.getValue( xr, seq_cds.asResidue(y) )
if s < 0:
raise ValueError("mis-matching residues.")
map_p2c.addPair( x, y, float(s) )
# advance to next residues
x += 1
y += 1
# sanity checks
assert( map_p2c.getRowTo() <= seq_wobble.getLength() )
assert( map_p2c.getColTo() <= seq_cds.getLength() )
def FilterConflicts( old_predictions, new_predictions, removed_predictions,
min_overlap, peptide_sequences):
"""remove conflicts.
Remove overlapping entries between different queries.
Only remove those sequences, which are alignable.
If they are alignable, take the sequence with the highest score and highest coverage.
(Take both, if score and coverage are not correlated.)
"""
##################################################################################################
## sort predictions by genomic region
if isinstance( old_predictions, PredictionFile.PredictionFile):
old_predictions.sort( ('mSbjctToken', 'mSbjctStrand', 'mSbjctGenomeFrom', 'mSbjctGenomeTo' ) )
else:
old_predictions.sort( lambda x, y: cmp( (x.mSbjctToken, x.mSbjctStrand, x.mSbjctGenomeFrom, x.mSbjctGenomeTo),
(y.mSbjctToken, y.mSbjctStrand, y.mSbjctGenomeFrom, y.mSbjctGenomeTo) ))
##################################################################################################
## filter predictions and resolve conflicts based on genomic overlap
## deleted segments are put in a temporary storage space.
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL, param_gop, param_gep )
result = alignlib.makeAlignmentVector()
alignments = {}
noverlaps = 0
nredundants = 0
nnew = 0
last_prediction = None
for this_prediction in old_predictions:
try:
this_query_peptide, this_query_status, this_query_gene, this_query_transcript = \
re.split("\s+", this_prediction.mQueryToken)
except ValueError:
this_query_gene = None
if not last_prediction:
last_prediction = this_prediction
last_query_gene = this_query_gene
continue
overlap = min(last_prediction.mSbjctGenomeTo, this_prediction.mSbjctGenomeTo) - \
max(last_prediction.mSbjctGenomeFrom, this_prediction.mSbjctGenomeFrom)
union = max(last_prediction.mSbjctGenomeTo, this_prediction.mSbjctGenomeTo) - \
min(last_prediction.mSbjctGenomeFrom, this_prediction.mSbjctGenomeFrom)
# resolve overlap between different genes
if overlap > 0 and \
(last_query_gene != this_query_gene or last_query_gene == None):
noverlaps += 1
relative_overlap = 100 * overlap / union
# Start conflict resolution, if overlap is above threshold.
# Keep higher scoring segment.
#
# Check if queries are homologous.
if relative_overlap >= param_max_percent_overlap:
if peptide_sequences:
if last_prediction.mQueryToken < this_prediction.mQueryToken:
key = "%s-%s" % (last_prediction.mQueryToken, this_prediction.mQueryToken)
else:
key = "%s-%s" % (this_prediction.mQueryToken, last_prediction.mQueryToken)
if not alignments.has_key( key ):
result.clear()
alignator.align( result,
alignlib.makeSequence( peptide_sequences[this_prediction.mQueryToken]),
alignlib.makeSequence( peptide_sequences[last_prediction.mQueryToken]) )
alignments[key] = result.getScore()
if result.getScore() >= param_min_score_overlap:
nredundants += 1
if alignments[key] >= param_min_score_overlap:
is_overlap = 1
else:
is_overlap = 0
else:
is_overlap = 1
else:
is_overlap = 0
else:
is_overlap = 0
if is_overlap:
# take best prediction. If difference is very small, set
# difference to 0 (difference does not matter). In this case,
# the first prediction is taken.
d1 = last_prediction.mQueryCoverage - this_prediction.mQueryCoverage
if float(abs(d1)) / float(last_prediction.mQueryCoverage) < param_conflicts_min_difference: d1 = 0
d2 = last_prediction.score - this_prediction.score
if float(abs(d2)) / float(this_prediction.score) < param_conflicts_min_difference: d2 = 0
if d1 >= 0 and d2 >= 0:
if param_loglevel >= 2:
print "# CONFLICT: kept %i(%s-%i), overlap=%i(%5.2f), removed: %s" % (last_prediction.mPredictionId,
last_prediction.mQueryToken,
last_prediction.mSbjctGenomeFrom,
overlap, relative_overlap,
str(this_prediction))
if param_benchmarks:
if CheckBenchmark( this_prediction, last_prediction ):
print "# BENCHMARK KEPT with overlap=%i(%5.2f): %s" % ( overlap, relative_overlap,
str(last_prediction))
removed_predictions.append( this_prediction )
continue
elif d1 <= 0 and d2 <= 0:
if param_loglevel >= 2:
print "# CONFLICT: kept %i(%s-%i), overlap=%i(%5.2f), removed: %s" % (this_prediction.mPredictionId,
this_prediction.mQueryToken,
this_prediction.mSbjctGenomeFrom,
overlap, relative_overlap,
str(last_prediction))
if param_benchmarks:
if CheckBenchmark( last_prediction, this_prediction ):
print "# BENCHMARK KEPT with overlap=%i(%5.2f): %s" % ( overlap, relative_overlap,
str(this_prediction))
removed_predictions.append( last_prediction )
last_prediction = this_prediction
last_query_gene = this_query_gene
continue
else:
if param_loglevel >= 2:
print "# CONFLICT: non-correlated score/coverage. Keeping both %i(%s-%i) (%5.2f/%i/%i) and %i(%s-%i) (%5.2f/%i/%i)" % \
(this_prediction.mPredictionId,
this_prediction.mQueryToken, this_prediction.mSbjctGenomeFrom,
this_prediction.score, this_prediction.mQueryCoverage,
this_prediction.mPercentIdentity,
last_prediction.mPredictionId,
last_prediction.mQueryToken, last_prediction.mSbjctGenomeFrom,
last_prediction.score, last_prediction.mQueryCoverage,
last_prediction.mPercentIdentity)
new_predictions.append(last_prediction)
nnew += 1
last_query_gene = this_query_gene
last_prediction = this_prediction
new_predictions.append(last_prediction)
nnew += 1
if param_loglevel >= 1:
print "# calculated %i alignments for %i potential conflicts (%i above threshold)" % \
(len(alignments), noverlaps, nredundants)
return nnew
def getAlignmentFull( m, q, t, options ):
"""print alignment with gaps in both query and target."""
a = alignlib.AlignmentFormatExplicit( m, alignlib.makeSequence(q), alignlib.makeSequence(t) )
return a.mRowAlignment, a.mColAlignment
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
def buildMapPdb2Sequence( sequence, filename_pdb, options, pdb_chain = ""):
"""build a map for residue numbers in pdb file to residue numbers on
a sequence.
returns the following maps:
map_structure2seq: mapping of residue numbers between structure and
sequence. These are mappings that will work if you "renumber" the
structure.
map_pdb2seq, map_seq2pdb: mapping according to residue numbers in pdb file.
"""
if not os.path.exists( filename_pdb ):
return None, None
structure = Scientific.IO.PDB.Structure( filename_pdb )
map_pdb2seq = {}
map_seq2pdb = {}
for chain in structure.peptide_chains:
if chain.chain_id == pdb_chain:
## align pdb sequence to sequence
map_structure2seq = alignlib.makeAlignataVector()
alignator = alignlib.makeFullDP( -10.0, -2.0 )
## build sequence of pdb file
structure = ""
for residue in chain.sequence():
structure += AMINOACIDS[residue]
## align reference sequence to sequence of pdb file
row = alignlib.makeSequence( structure )
col = alignlib.makeSequence( sequence )
alignator.Align(row, col, map_structure2seq)
if options.loglevel >= 3:
options.stdlog.write( "structure: %s\n" % structure )
options.stdlog.write( "sequence : %s\n" % sequence )
options.stdlog.write( "alignment of structure to sequence:\n" )
options.stdlog.write( alignlib.writePairAlignment( row, col, map_structure2seq ) + "\n" )
# print alignlib.writeAlignataTable(map_structure2seq)
residue_number = 0
for residue in chain.residues:
residue_number += 1
mapped_residue = map_structure2seq.mapRowToCol(residue_number)
if not mapped_residue:
if options.loglevel >= 3:
options.stdlog.write( "# skipped residue %s=%s %i\n" % (str(residue.number), residue.name, residue_number))
continue
r = str(residue.number)
map_pdb2seq[r] = mapped_residue
map_seq2pdb[mapped_residue] = r
return map_structure2seq, map_pdb2seq, map_seq2pdb, residue_number-1, str(chain.residues[0].number), str(chain.residues[-1].number), structure
tmali.apply( translate )
tmap_mali = Mali.Mali()
tmap_mali.readFromFile( open(options.filename_map_mali, "r") )
if tmap_mali.getAlphabet() == "na":
tmap_mali.apply( translate )
map_old2new = alignlib.makeAlignmentVector()
mali1 = alignlib.makeProfileFromMali( convertMali2Mali( tmali ) )
if tmap_mali.getLength() == 1:
s = tmap_mali.values()[0].mString
mali2 = alignlib.makeSequence( s )
## see if you can find an identical subsequence and then align to thisD
for x in tmali.values():
if s in re.sub( "[- .]+", "", x.mString):
mali1 = alignlib.makeSequence( x.mString )
break
else:
mali2 = alignlib.makeProfileFromMali( convertMali2Mali( tmap_mali ) )
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL, -10.0, -2.0 )
alignator.align( map_old2new, mali1, mali2 )
consensus = tmap_mali.getConsensus()
if options.loglevel >= 4:
options.stdlog.write( "# alphabet: %s\n" % tmap_mali.getAlphabet() )
filename_sequences = None,
format = "fasta",
)
(options, args) = E.Start( parser )
if not options.filename_sequences:
raise "please supply filename with sequences."
sequences = Genomics.ReadPeptideSequences( open(options.filename_sequences, "r") )
if options.loglevel >= 1:
print "# read %i sequences" % len(sequences)
for k in sequences.keys():
sequences[k] = alignlib.makeSequence( sequences[k] )
if options.loglevel >= 2:
print "# converted %i sequences" % len(sequences)
ninput, noutput, nskipped, nfailed = 0, 0, 0, 0
link = BlastAlignments.Link()
ali = alignlib.makeAlignataVector()
for line in sys.stdin:
if line[0] == "#": continue
link.Read( line )
ninput += 1
def align(self, query, sbjct, map_query2sbjct):
xrow = alignlib.makeSequence(query.asString())
xcol = alignlib.makeSequence(sbjct.asString())
self.mAlignator.align( xrow, xcol, map_query2sbjct)
print "version="
sys.exit(0)
elif o in ( "-h", "--help" ):
print globals()["__doc__"]
sys.exit(0)
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL, param_gop, param_gep )
map_query2token = alignlib.makeAlignmentVector()
for line in sys.stdin:
if line[0] == "#": continue
query_token, sbjct_token, query_sequence, sbjct_sequence = string.split(line[:-1], "\t")
map_query2token.clear()
row = alignlib.makeSequence(query_sequence)
col = alignlib.makeSequence(sbjct_sequence)
alignator.align( map_query2token, row, col )
pidentity = 100.0 * alignlib.calculatePercentIdentity( map_query2token, row, col )
psimilarity = 100.0 * alignlib.calculatePercentSimilarity( map_query2token )
print string.join( map(str, (
query_token, sbjct_token,
map_query2token.getScore(),
alignlib.AlignmentFormatEmissions( map_query2token ),
pidentity,
psimilarity,
map_query2token.getNumGaps()) ), "\t" )
def ProcessRegion( predictions, region_id, region,
peptide_sequences = None,
filter_queries = {} ):
"""process a set of matches to a region.
resolve region according to homology.
"""
if options.loglevel >= 3:
options.stdlog.write( "###################################################################\n" )
options.stdlog.write( "# resolving %i predictions in region %s\n" % ( len(predictions), str(region)) )
sys.stdout.flush()
predictions.sort( lambda x,y: cmp(x.score, y.score))
predictions.reverse()
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL, options.gop, options.gep )
result = alignlib.makeAlignmentVector()
cluster = []
map_sequence2cluster = range(0,len(predictions))
edges = []
noutput, nskipped = 0, 0
if peptide_sequences:
for x in range(len(predictions)):
if options.loglevel >= 5:
options.stdlog.write( "# filtering from %i with prediction %i: %s\n" % (x, predictions[x].mPredictionId, predictions[x].mQueryToken) )
sys.stdout.flush()
if map_sequence2cluster[x] != x: continue
region_id += 1
edges = []
if predictions[x].mQueryToken not in filter_queries:
edges.append( predictions[x] )
else:
nskipped += 1
for y in range(x+1,len(predictions)):
if map_sequence2cluster[y] != y: continue
if predictions[x].mQueryToken < predictions[y].mQueryToken:
key = "%s-%s" % (predictions[x].mQueryToken, predictions[y].mQueryToken)
else:
key = "%s-%s" % (predictions[y].mQueryToken, predictions[x].mQueryToken)
# check if predictions are overlapping on the genomic sequence
if min(predictions[x].mSbjctGenomeTo, predictions[y].mSbjctGenomeTo) - \
max(predictions[x].mSbjctGenomeFrom, predictions[y].mSbjctGenomeFrom) < 0:
if options.loglevel >= 4:
options.stdlog.write( "# alignment of predictions %i and %i: no overlap on genomic sequence, thus skipped\n" %\
(predictions[x].mPredictionId,
predictions[y].mPredictionId ) )
sys.stdout.flush()
continue
if not global_alignments.has_key( key ):
seq1 = peptide_sequences[predictions[x].mQueryToken]
seq2 = peptide_sequences[predictions[y].mQueryToken]
result.clear()
s1 = alignlib.makeSequence( seq1 )
s2 = alignlib.makeSequence( seq2 )
alignator.align( result, s1, s2 )
c1 = 100 * (result.getRowTo() - result.getRowFrom()) / len(seq1)
c2 = 100 * (result.getColTo() - result.getColFrom()) / len(seq2)
min_cov = min(c1,c2)
max_cov = max(c1,c2)
identity = alignlib.calculatePercentIdentity( result, s1, s2 ) * 100
# check if predictions overlap and they are homologous
if result.getScore() >= options.overlap_min_score and \
max_cov >= options.overlap_max_coverage and \
min_cov >= options.overlap_min_coverage and \
identity >= options.overlap_min_identity :
global_alignments[key] = True
else:
global_alignments[key] = False
if options.loglevel >= 4:
options.stdlog.write( "# alignment=%s score=%i pid=%5.2f c1=%i c2=%i min_cov=%i max_cov=%i homolog=%s\n" %\
(key,
result.getScore(),
identity,
c1,c2, min_cov, max_cov,
global_alignments[key]) )
sys.stdout.flush()
if global_alignments[key]:
map_sequence2cluster[y] = x
if predictions[y].mQueryToken not in filter_queries:
edges.append( predictions[y] )
else:
nskipped += 1
noutput += PrintEdges( region_id, region, edges )
return region_id, noutput, nskipped
def _alignToProfile(infile, outfile, min_score=0):
'''align sequences in *infile* against mali
Only alignments with a score higher than *min_score* are accepted.
Output multiple alignment in fasta format to *outfile* and a table
in :file:`outfile.log`.
'''
mali = Mali.Mali()
mali.readFromFile(open("../data/mouse.fasta"))
src_mali = Mali.convertMali2Alignlib(mali)
E.debug("read mali: %i sequences x %i columns" %
(mali.getNumSequences(), mali.getNumColumns()))
# add pseudocounts
profile_mali = mali.getClone()
n = profile_mali.getNumColumns()
for x in "ACGT":
for y in range(0, 2):
profile_mali.addSequence("%s%i" % (x, y), 0, n, x * n)
profile_mali = Mali.convertMali2Alignlib(profile_mali)
alignlib.setDefaultEncoder(alignlib.getEncoder(alignlib.DNA4))
alignlib.setDefaultLogOddor(alignlib.makeLogOddorUniform())
# bg = alignlib.FrequencyVector()
# bg.extend( ( 0.3, 0.1, 0.2, 0.2, 0.2) )
# alignlib.setDefaultRegularizor( alignlib.makeRegularizorTatusov(
# alignlib.makeSubstitutionMatrixDNA4(),
# bg,
# "ACGTN",
# 10.0, 1.0) )
profile = alignlib.makeProfile(profile_mali)
alignment_mode = alignlib.ALIGNMENT_WRAP
alignator = alignlib.makeAlignatorDPFull(alignment_mode, -5.0, -0.5)
map_seq2profile = alignlib.makeAlignmentVector()
map_rseq2profile = alignlib.makeAlignmentVector()
profile.prepare()
# print profile
build_mali = alignlib.makeMultAlignment()
m = alignlib.makeAlignmentVector()
m.addDiagonal(0, n, 0)
build_mali.add(src_mali, m)
outf = open(outfile, "w")
outf_log = open(outfile + ".info", "w")
outf_log.write(
"read_id\tlength\tstart\tend\tparts\tcovered\tpcovered\tscore\tmali_start\tmali_end\tmali_covered\tmali_pcovered\n"
)
sequences, aa = alignlib.StringVector(), alignlib.AlignandumVector()
ids = []
for pid in mali.getIdentifiers():
sequences.append(re.sub("-", "", mali[pid]))
ids.append(pid)
# print str(alignlib.MultAlignmentFormatPlain( build_mali, sequences ))
c = E.Counter()
for s in FastaIterator.FastaIterator(open(infile)):
E.debug("adding %s" % s.title)
c.input += 1
rsequence = Genomics.complement(s.sequence)
seq = alignlib.makeSequence(s.sequence)
rseq = alignlib.makeSequence(rsequence)
alignator.align(map_seq2profile, seq, profile)
alignator.align(map_rseq2profile, rseq, profile)
if map_seq2profile.getScore() > map_rseq2profile.getScore():
m, seq, sequence = map_seq2profile, seq, s.sequence
else:
m, seq, sequence = map_rseq2profile, rseq, rsequence
if m.getLength() == 0:
c.skipped += 1
continue
if m.getScore() < min_score:
c.skipped += 1
continue
r = getParts(m)
covered = 0
for mm in r:
build_mali.add(mm)
sequences.append(sequence)
ids.append(s.title)
covered += mm.getLength() - mm.getNumGaps()
mali_covered = m.getColTo() - m.getColFrom()
outf_log.write("\t".join(
map(str, (s.title, len(s.sequence), m.getRowFrom(), m.getRowTo(),
len(r), covered, "%5.2f" %
(100.0 * covered / len(s.sequence)), m.getScore(),
m.getColFrom(), m.getColTo(), mali_covered, "%5.2f" %
((100.0 * mali_covered) / mali.getNumColumns())))) +
"\n")
c.output += 1
#build_mali.expand( aa )
result = str(
alignlib.MultAlignmentFormatPlain(build_mali, sequences,
alignlib.UnalignedStacked))
for pid, data in zip(ids, result.split("\n")):
start, sequence, end = data.split("\t")
outf.write(">%s/%i-%i\n%s\n" %
(pid, int(start) + 1, int(end), sequence))
outf.close()
outf_log.close()
E.info("%s\n" % str(c))
def _alignToProfile( infile, outfile,
min_score = 0 ):
'''align sequences in *infile* against mali
Only alignments with a score higher than *min_score* are accepted.
Output multiple alignment in fasta format to *outfile* and a table
in :file:`outfile.log`.
'''
mali = Mali.Mali()
mali.readFromFile( open("../data/mouse.fasta") )
src_mali = Mali.convertMali2Alignlib( mali )
E.debug( "read mali: %i sequences x %i columns" % (mali.getNumSequences(), mali.getNumColumns() ))
# add pseudocounts
profile_mali = mali.getClone()
n = profile_mali.getNumColumns()
for x in "ACGT":
for y in range(0,2):
profile_mali.addSequence( "%s%i" % (x,y), 0, n, x * n )
profile_mali = Mali.convertMali2Alignlib( profile_mali )
alignlib.setDefaultEncoder( alignlib.getEncoder( alignlib.DNA4 ) )
alignlib.setDefaultLogOddor( alignlib.makeLogOddorUniform() )
# bg = alignlib.FrequencyVector()
# bg.extend( ( 0.3, 0.1, 0.2, 0.2, 0.2) )
# alignlib.setDefaultRegularizor( alignlib.makeRegularizorTatusov(
# alignlib.makeSubstitutionMatrixDNA4(),
# bg,
# "ACGTN",
# 10.0, 1.0) )
profile = alignlib.makeProfile( profile_mali )
alignment_mode = alignlib.ALIGNMENT_WRAP
alignator = alignlib.makeAlignatorDPFull( alignment_mode,
-5.0,
-0.5 )
map_seq2profile = alignlib.makeAlignmentVector()
map_rseq2profile = alignlib.makeAlignmentVector()
profile.prepare()
# print profile
build_mali = alignlib.makeMultAlignment()
m = alignlib.makeAlignmentVector()
m.addDiagonal( 0, n, 0 )
build_mali.add( src_mali, m )
outf = open( outfile, "w" )
outf_log = open( outfile + ".info", "w" )
outf_log.write( "read_id\tlength\tstart\tend\tparts\tcovered\tpcovered\tscore\tmali_start\tmali_end\tmali_covered\tmali_pcovered\n" )
sequences, aa = alignlib.StringVector(), alignlib.AlignandumVector()
ids = []
for pid in mali.getIdentifiers():
sequences.append( re.sub( "-", "", mali[pid] ) )
ids.append( pid )
# print str(alignlib.MultAlignmentFormatPlain( build_mali, sequences ))
c = E.Counter()
for s in FastaIterator.FastaIterator( open(infile)):
E.debug("adding %s" % s.title )
c.input += 1
rsequence = Genomics.complement(s.sequence)
seq = alignlib.makeSequence( s.sequence )
rseq = alignlib.makeSequence( rsequence )
alignator.align( map_seq2profile, seq, profile )
alignator.align( map_rseq2profile, rseq, profile )
if map_seq2profile.getScore() > map_rseq2profile.getScore():
m, seq, sequence = map_seq2profile, seq, s.sequence
else:
m, seq, sequence = map_rseq2profile, rseq, rsequence
if m.getLength() == 0:
c.skipped += 1
continue
if m.getScore() < min_score:
c.skipped += 1
continue
r = getParts( m )
covered = 0
for mm in r:
build_mali.add( mm )
sequences.append( sequence )
ids.append( s.title )
covered += mm.getLength() - mm.getNumGaps()
mali_covered = m.getColTo() - m.getColFrom()
outf_log.write( "\t".join( map(str, (
s.title,
len(s.sequence),
m.getRowFrom(),
m.getRowTo(),
len(r),
covered,
"%5.2f" % (100.0 * covered / len(s.sequence) ),
m.getScore(),
m.getColFrom(),
m.getColTo(),
mali_covered,
"%5.2f" % ((100.0 * mali_covered) / mali.getNumColumns())
) ) ) + "\n" )
c.output += 1
#build_mali.expand( aa )
result = str(alignlib.MultAlignmentFormatPlain( build_mali,
sequences,
alignlib.UnalignedStacked ))
for pid, data in zip(ids, result.split("\n") ):
start, sequence, end = data.split("\t")
outf.write(">%s/%i-%i\n%s\n" % (pid, int(start)+1, int(end), sequence) )
outf.close()
outf_log.close()
E.info( "%s\n" % str(c) )
def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser( version = "%prog version: $Id: gpipe/compare_predictions2exons.py 2011 2008-07-04 10:40:51Z andreas $",
usage = globals()["__doc__"] )
parser.add_option( "-g", "--genome-file", dest="genome_file", type="string",
help="filename with genome." )
parser.add_option( "-b", "--boundaries", dest="filename_boundaries", type="string",
help="filename with exon boundaries." )
parser.add_option( "-e", "--exons", dest="filename_exons", type="string",
help="filename with exons (output)." )
parser.add_option( "-p", "--peptides", dest="filename_peptides", type="string",
help="filename with peptide sequences." )
parser.add_option( "-w", "--write-notfound", dest="write_notfound", action="store_true",
help="print exons for predictions not found in reference." )
parser.add_option( "-q", "--quality-pide", dest="quality_threshold_pide", type="int",
help="quality threshold (pide) for exons." )
parser.set_defaults(
genome_file = "genome",
filename_boundaries = None,
filename_exons = None,
filename_peptides = None,
quality_threshold_pide = 0,
write_notfound = False,
## allowed number of nucleotides for exon boundaries to
## be considered equivalent.
slipping_exon_boundary = 9,
## stop codons to search for
stop_codons = ("TAG", "TAA", "TGA"), )
(options, args) = E.Start( parser, add_pipe_options = True )
if len(args) > 0:
print USAGE, "no arguments required."
sys.exit(2)
reference_exon_boundaries = {}
if options.filename_boundaries:
reference_exon_boundaries = Exons.ReadExonBoundaries( open( options.filename_boundaries, "r"),
do_invert = 1,
remove_utr = 1)
E.info( "read exon boundaries for %i queries" % len(reference_exon_boundaries) )
if options.filename_exons:
outfile_exons = open( options.filename_exons, "w")
outfile_exons.write( "%s\n" % "\t".join( (
"prediction_id",
"exon_id",
"exon_from",
"exon_to",
"exon_frame",
"reference_id",
"reference_from",
"reference_to",
"reference_phase",
"pidentity",
"psimilarity",
"nframeshifts",
"ngaps",
"nstopcodons",
"is_ok",
"genome_exon_from",
"genome_exon_to") ) )
else:
outfile_exons = None
if options.filename_peptides:
peptide_sequences = Genomics.ReadPeptideSequences( open(options.filename_peptides, "r") )
E.info("read peptide sequences for %i queries" % len(peptide_sequences) )
else:
peptide_sequences = {}
entry = PredictionParser.PredictionParserEntry()
last_filename_genome = None
nfound, nmissed_exons, nmissed_length = 0, 0, 0
nempty_alignments = 0
fasta = IndexedFasta.IndexedFasta( options.genome_file )
options.stdout.write( "%s\n" % "\t".join( (
"prediction_id",
"number",
"dubious_exons",
"boundaries_sum",
"boundaries_max",
"identical_exons",
"inserted_exons",
"deleted_exons",
"inserted_introns",
"deleted_introns",
"truncated_Nterminus",
"truncated_Cterminus",
"deleted_Nexons",
"deleted_Cexons",
"inserted_Nexons",
"inserted_Cexons" ) ) )
for line in sys.stdin:
if line[0] == "#": continue
try:
entry.Read(line)
except ValueError, msg:
print "# parsing failed with msg %s in line %s" % (msg, line[:-1])
sys.exit(1)
exons = Genomics.Alignment2ExonBoundaries( entry.mMapPeptide2Genome,
query_from = entry.mQueryFrom,
sbjct_from = entry.mSbjctGenomeFrom,
add_stop_codon = 0 )
if exons[-1][4] != entry.mSbjctGenomeTo:
print "# WARNING: discrepancy in exon calculation!!!"
for e in exons:
print "#", str(e)
print "#", str(entry)
if options.loglevel >= 5:
for e in exons:
print "#", str(e)
genomic_fragment = fasta.getSequence( entry.mSbjctToken, entry.mSbjctStrand,
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo )
skip = False
if peptide_sequences.has_key( entry.mQueryToken ):
query_sequence = alignlib.makeSequence(peptide_sequences[entry.mQueryToken])
sbjct_sequence = alignlib.makeSequence(entry.mTranslation)
percent_similarity, percent_identity = 0, 0
if query_sequence.getLength() < entry.mMapPeptide2Translation.getRowTo():
print "# WARNING: query sequence %s is too short: %i %i" % ( entry.mQueryToken,
query_sequence.getLength(),
entry.mMapPeptide2Translation.getRowTo())
sys.stdout.flush()
nmissed_length += 1
skip = True
elif sbjct_sequence.getLength() < entry.mMapPeptide2Translation.getColTo():
print "# WARNING: sbjct sequence %s is too short: %i %i" % ( entry.mSbjctToken,
sbjct_sequence.getLength(),
entry.mMapPeptide2Translation.getColTo())
sys.stdout.flush()
nmissed_length += 1
skip = True
else:
alignlib.rescoreAlignment( entry.mMapPeptide2Translation,
query_sequence,
sbjct_sequence,
alignlib.makeScorer( query_sequence, sbjct_sequence ) )
percent_identity = alignlib.calculatePercentIdentity( entry.mMapPeptide2Translation,
query_sequence,
sbjct_sequence ) * 100
percent_similarity = alignlib.calculatePercentSimilarity( entry.mMapPeptide2Translation ) * 100
E.debug( "prediction %s: percent identity/similarity: before=%5.2f/%5.2f, realigned=%5.2f/%5.2f" % (
str(entry.mPredictionId),
entry.mPercentSimilarity,
entry.mPercentIdentity,
percent_similarity,
percent_identity ) )
else:
query_sequence = None
sbjct_sequence = None
# default values
exons_num_exons = "na"
exons_boundaries_sum = "na"
exons_boundaries_max = "na"
dubious_exons = "na"
ndeleted_exons, ninserted_exons, ndeleted_introns, ninserted_introns, nidentical_exons = 0,0,0,0,0
truncated_Nterminal_exon, truncated_Cterminal_exon = 0,0
ndeleted_Nexons, ndeleted_Cexons = 0, 0
ninserted_Nexons, ninserted_Cexons = 0, 0
exons_offset = exons[0][3]
if not reference_exon_boundaries.has_key( entry.mQueryToken ):
print "# WARNING: sequence %s has no exon boundaries" % ( entry.mQueryToken )
sys.stdout.flush()
nmissed_exons += 1
skip = True
if not skip:
nfound += 1
ref_exons = reference_exon_boundaries[entry.mQueryToken]
ref_exons_offset = ref_exons[0].mGenomeFrom
exons_num_exons = len(ref_exons) - len(exons)
exons_boundaries_sum = 0
exons_phase = 0
exons_boundaries_max = 0
dubious_exons = 0
inserted_exons = 0
temp_inserted_exons = 0
if options.loglevel >= 3:
for e in exons:
options.stdlog.write( "# %s\n" % str(e) )
for e in ref_exons:
options.stdlog.write( "# %s\n" % str(e) )
min_pide = entry.mPercentIdentity * options.quality_threshold_pide / 100
in_sync = 0
e,r = 0,0
while e < len(exons) and r < len(ref_exons):
this_e, this_r = e+1, r+1
percent_identity = 0
percent_similarity = 0
is_good_exon = 0
if options.loglevel >= 4:
options.stdlog.write( "# current exons: %i and %i\n" % (e, r) )
sys.stdout.flush()
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to, exon_ali = exons[e][0:6]
ref_from, ref_to, ref_phase, ref_genome_from, ref_genome_to = (ref_exons[r].mPeptideFrom,
ref_exons[r].mPeptideTo,
ref_exons[r].frame,
ref_exons[r].mGenomeFrom,
ref_exons[r].mGenomeTo)
ref_genome_from -= ref_exons_offset
ref_genome_to -= ref_exons_offset
## get percent identity for exon
exon_percent_identity = 0
exon_percent_similarity = 0
if query_sequence and sbjct_sequence:
tmp_ali = alignlib.makeAlignmentVector()
xquery_from = exon_from / 3
xquery_to = exon_to / 3
alignlib.copyAlignment( tmp_ali, entry.mMapPeptide2Translation, xquery_from, xquery_to )
if tmp_ali.getLength() == 0:
options.stdlog.write( "# WARNING: empty alignment %s\n" % str((ref_from, exon_from, ref_to, exon_to, xquery_from, xquery_to)))
nempty_alignments += 1
else:
if options.loglevel >= 5:
options.stdlog.write( "# %s\n" % str( alignlib.AlignmentFormatExplicit( tmp_ali, query_sequence, sbjct_sequence ) ) )
exon_percent_identity = alignlib.calculatePercentIdentity( tmp_ali,
query_sequence,
sbjct_sequence ) * 100
exon_percent_similarity = alignlib.calculatePercentSimilarity( tmp_ali ) * 100
if exon_percent_identity >= min_pide:
is_good_exon = 1
else:
is_good_exon = 0
if e < len(exons) -1 :
(next_exon_from, next_exon_to, next_exon_phase,
next_exon_genome_from, next_exon_genome_to, next_exon_ali) = exons[e+1][0:6]
else:
(next_exon_from, next_exon_to, next_exon_phase,
next_exon_genome_from, next_exon_genome_to, next_exon_ali) = 0, 0, 0, 0, 0, []
if r < len(ref_exons) - 1:
next_ref_from, next_ref_to, next_ref_phase = (ref_exons[r+1].mPeptideFrom,
ref_exons[r+1].mPeptideTo,
ref_exons[r+1].frame)
else:
next_ref_from, next_ref_to, next_ref_phase = 0, 0, 0
if options.loglevel >= 2:
options.stdlog.write( "# %s\n" % "\t".join( map(str, (entry.mQueryToken,
exon_from, exon_to, exon_phase,
exon_genome_from, exon_genome_to,
ref_from, ref_to, ref_phase ))))
sys.stdout.flush()
# beware of small exons.
# if less than options.slipping_exon_boundary: boundary is 0
# check if end is more than options.splipping_exon_boundary apart as well.
if exon_to - exon_from <= options.slipping_exon_boundary or \
ref_to - ref_from <= options.slipping_exon_boundary:
boundary = 0
else:
boundary = options.slipping_exon_boundary
if ref_to <= exon_from + boundary and \
ref_to <= exon_to - options.slipping_exon_boundary:
## no overlap
is_good_exon = 0
if e == 0:
ndeleted_Nexons += 1
else:
ndeleted_exons += 1
r += 1
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to = 0, 0, 0, 0, 0
overlap = 0
elif exon_to <= ref_from + boundary and \
exon_to <= ref_to - options.slipping_exon_boundary:
## no overlap
is_good_exon = 0
if r == 0:
ninserted_Nexons += 1
else:
ninserted_exons += 1
e += 1
ref_from, ref_to, ref_phase = 0, 0, 0
overlap = 0
else:
## overlap
overlap = 1
dfrom = int(math.fabs(exon_from - ref_from))
dto = int(math.fabs(exon_to - ref_to))
## get percent identity for overlapping fragment
if query_sequence and sbjct_sequence:
## this the problem
tmp_ali = alignlib.makeAlignmentVector()
xquery_from = max( ref_from / 3, exon_from / 3)
xquery_to = min(ref_to / 3, exon_to / 3)
alignlib.copyAlignment( tmp_ali, entry.mMapPeptide2Translation, xquery_from, xquery_to )
if tmp_ali.getLength() == 0:
options.stdlog.write( "# warning: empty alignment %s\n" % str((ref_from, exon_from, ref_to, exon_to, xquery_from, xquery_to )))
percent_identity = 0
percent_similarity = 0
else:
if options.loglevel >= 5:
print str( alignlib.AlignmentFormatExplicit( tmp_ali, query_sequence, sbjct_sequence ) )
percent_identity = alignlib.calculatePercentIdentity( tmp_ali,
query_sequence,
sbjct_sequence ) * 100
percent_similarity = alignlib.calculatePercentSimilarity( tmp_ali ) * 100
if percent_identity >= min_pide:
is_good_exon = 1
else:
is_good_exon = 0
dubious_exons += 1
## adjust regions for terminal exons
if e == 0 and r == 0 and dfrom <= (entry.mQueryFrom - 1) * 3 and dfrom > 0:
if is_good_exon:
truncated_Nterminal_exon = dfrom
dfrom = 0
## truncated terminal exons
if e == len(exons)-1 and r == len(ref_exons)-1 and dto <= (entry.mQueryLength - entry.mQueryTo) * 3 and dto > 0:
if is_good_exon:
truncated_Cterminal_exon = dto
dto = 0
## do not count deviations for terminal query exons
if e == 0 and dfrom <= entry.mQueryFrom * 3 and dfrom > 0:
dfrom = 0
if e == len(exons)-1 and dto <= (entry.mQueryLength - entry.mQueryTo) * 3 and dto > 0:
dto = 0
## permit difference of one codon (assumed to be stop)
if e == len(exons)-1 and r == len(ref_exons)-1 and dto == 3:
dto = 0
## deal with different boundary conditions:
if dfrom == 0 and dto == 0:
if is_good_exon: nidentical_exons += 1
e += 1
r += 1
## next exon within this ref_exon
elif exon_to < ref_to and next_exon_to and next_exon_to <= ref_to + options.slipping_exon_boundary:
if is_good_exon: ninserted_introns += 1
e += 1
in_sync = 1
dto = 0
## next ref_exon within this exon
elif ref_to < exon_to and next_ref_to and next_ref_to <= exon_to + options.slipping_exon_boundary:
if is_good_exon: ndeleted_introns += 1
r += 1
in_sync = 1
dto = 0
else:
e += 1
r += 1
if in_sync:
dfrom = 0
if is_good_exon:
exons_boundaries_sum += dfrom + dto
exons_boundaries_max = max( dfrom, exons_boundaries_max )
exons_boundaries_max = max( dto, exons_boundaries_max )
###########################################################
## count inserted/deleted introns and misplaced boundaries
##
## if exon and next_exon in ref_exon: inserted intron
## if ref_exon and next_ref_exon in exon: deleted intron
if outfile_exons:
if genomic_fragment and exon_genome_to:
nintrons, nframeshifts, ngaps, nsplits, nstopcodons, disruptions = Genomics.CountGeneFeatures( exon_genome_from - entry.mSbjctGenomeFrom,
exon_ali,
genomic_fragment,
border_stop_codon = 0
)
else:
nintrons, nframeshifts, ngaps, nsplits, nstopcodons = 0, 0, 0, 0, 0
if exon_to == 0: this_e = 0
if ref_to == 0: this_r = 0
outfile_exons.write( string.join( map(str, (entry.mPredictionId,
this_e, exon_from, exon_to, exon_phase,
this_r, ref_from, ref_to, ref_phase,
percent_identity, percent_similarity,
nframeshifts, ngaps, nstopcodons,
is_good_exon,
exon_genome_from, exon_genome_to,
)), "\t") + "\n")
while e < len(exons):
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to = exons[e][0:5]
e += 1
ninserted_Cexons += 1
if outfile_exons:
outfile_exons.write( string.join( map(str, (entry.mPredictionId,
e, exon_from, exon_to, exon_phase,
0, 0, 0, 0,
0, 0,
0, 0, 0,
1,
exon_genome_from, exon_genome_to,
)), "\t") + "\n")
while r < len(ref_exons):
ref_from, ref_to, ref_phase, ref_genome_from, ref_genome_to = (ref_exons[r].mPeptideFrom,
ref_exons[r].mPeptideTo,
ref_exons[r].frame,
ref_exons[r].mGenomeFrom,
ref_exons[r].mGenomeTo)
ndeleted_Cexons += 1
ref_genome_from -= ref_exons_offset
ref_genome_to -= ref_exons_offset
r += 1
if outfile_exons:
outfile_exons.write( string.join( map(str, (entry.mPredictionId,
0, 0, 0, 0,
r, ref_from, ref_to, ref_phase,
0, 0,
0, 0, 0,
0,
0, 0,
)), "\t") + "\n")
else:
if options.write_notfound:
this_e = 0
## use prediction's identity/similarity for exons.
## This will still then flag stop-codons in later analysis
percent_identity = entry.mPercentIdentity
percent_similarity = entry.mPercentSimilarity
for exon in exons:
this_e += 1
exon_from, exon_to, exon_phase, exon_genome_from, exon_genome_to, exon_ali = exon[0:6]
if genomic_fragment:
nintrons, nframeshifts, ngaps, nsplits, nstopcodons, disruptions = Genomics.CountGeneFeatures( exon_genome_from - entry.mSbjctGenomeFrom,
exon_ali,
genomic_fragment )
outfile_exons.write( string.join( map(str, (entry.mPredictionId,
this_e, exon_from, exon_to, exon_phase,
0, 0, 0, 0,
percent_identity, percent_similarity,
nframeshifts, ngaps, nstopcodons,
1,
exon_genome_from, exon_genome_to,
)), "\t") + "\n")
options.stdout.write( "\t".join(map(str,
(entry.mPredictionId,
exons_num_exons,
dubious_exons,
exons_boundaries_sum,
exons_boundaries_max,
nidentical_exons,
ninserted_exons, ndeleted_exons,
ninserted_introns, ndeleted_introns,
truncated_Nterminal_exon, truncated_Cterminal_exon,
ndeleted_Nexons, ndeleted_Cexons,
ninserted_Nexons, ninserted_Cexons))) + "\n" )
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
(options, args) = E.Start( parser, add_pipe_options = True )
if options.filename_sequences:
infile = open(options.filename_sequences, "r")
else:
infile = sys.stdin
parser = FastaIterator.FastaIterator( infile )
sequences = []
while 1:
cur_record = iterator.next()
if cur_record is None: break
sequences.append( (cur_record.title, alignlib.makeSequence(re.sub( " ", "", cur_record.sequence)) ) )
if options.filename_sequences:
infile.close()
alignator = alignlib.makeAlignatorFullDP( options.gop, options.gep )
map_a2b = alignlib.makeAlignataVector()
nsequences = len(sequences)
for x in range(0,nsequences-1):
for y in range(x+1, nsequences):
alignator.Align( sequences[x][1], sequences[y][1], map_a2b)
row_ali, col_ali = alignlib.writeAlignataCompressed( map_a2b )
options.stdout.write( "%s\t%s\t%i\t%i\t%i\t%s\t%i\t%i\t%s\t%i\t%i\t%i\t%i\n" % (\
def PrintCluster( cluster,
cluster_id,
lengths,
peptide_sequences = None,
regex_preferred = None):
"""print a cluster.
Take longest sequence as representative. If preferred is given, only take
genes matching preferred identifier.
"""
if regex_preferred:
rx = re.compile(regex_preferred)
else:
rx = None
max_al = 0
max_pl = 0
rep_a = None
rep_p = None
for c in cluster:
l = 0
if c in lengths: l = lengths[c]
if l > max_al:
max_al = l
rep_a = c
if rx and rx.search(c) and l > max_pl:
max_pl = l
rep_p = c
if max_pl > 0:
max_l = max_pl
rep = rep_p
else:
max_l = max_al
rep = rep_a
for mem in cluster:
l = 0
if mem in lengths: l = lengths[mem]
if peptide_sequences:
map_rep2mem = alignlib.makeAlignmentVector()
if rep == mem and rep in lengths:
alignlib.addDiagonal2Alignment( map_rep2mem, 1, lengths[rep], 0)
elif mem in peptide_sequences and \
rep in peptide_sequences:
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL, -10.0, -1.0)
alignator.align( map_rep2mem,
alignlib.makeSequence( peptide_sequences[rep] ),
alignlib.makeSequence( peptide_sequences[mem] ) )
f = alignlib.AlignmentFormatEmissions( map_rep2mem )
print string.join( map(str, (rep, mem, l, f)), "\t" )
else:
print string.join( map(str, (rep, mem, l)), "\t" )
sys.stdout.flush()
return cluster_id
print "#", cds_fragment
print "# genomic"
print "#",genomic_fragment
continue
if map_query2sbjct.getRowTo() > len(cds_fragment):
print "# ERROR: length mismatch: cds fragment (%i) shorter than last aligned residue (%i)" %\
(len(cds_fragment), map_query2sbjct.getRowTo())
print "#", line
print "# cds"
print "#", cds_fragment
print "# genomic"
print "#",genomic_fragment
continue
cds_seq = alignlib.makeSequence( cds_fragment )
genomic_seq = alignlib.makeSequence( genomic_fragment )
data = map( lambda x: string.split(x, "\t"),
string.split( alignlib.writePairAlignment( cds_seq,
genomic_seq,
map_query2sbjct ), "\n" ))
row_ali, col_ali = Genomics.RemoveFrameShiftsFromAlignment(data[0][1], data[1][1])
row_ali = Genomics.MaskStopCodons( row_ali )
col_ali = Genomics.MaskStopCodons( col_ali )
if len(row_ali) != len(col_ali):
print "# ERROR: wrong alignment lengths."
def EliminateRedundantEntries( rep,
data,
eliminated_predictions,
options,
peptides,
extended_peptides,
filter_quality = None,
this_quality = None ):
"""eliminate redundant entries in a set."""
eliminated = []
rep_id = rep.transcript_id
rep_coverage, rep_pid = rep.mQueryCoverage, rep.mPid
alignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL, options.gop, options.gep )
result = alignlib.makeAlignmentVector()
rep_seq = peptides[rep_id]
rep_extended_seq = extended_peptides[rep_id]
for entry in data:
mem_id, mem_coverage, mem_pid, mem_quality = ( entry.transcript_id,
entry.mQueryCoverage,
entry.mPid,
entry.mQuality )
mem_seq = peptides[mem_id]
mem_extended_seq = extended_peptides[mem_id]
if options.loglevel >= 4:
options.stdlog.write( "# processing: id=%s class=%s\n" % (mem_id, mem_quality))
if mem_id in eliminated_predictions: continue
if mem_extended_seq == rep_extended_seq:
eliminated_predictions[mem_id] = rep_id
eliminated.append( (mem_id, "i") )
elif mem_extended_seq in rep_extended_seq:
eliminated_predictions[mem_id] = rep_id
eliminated.append( (mem_id, "p") )
else:
if mem_quality != this_quality or \
mem_quality in options.quality_exclude_same:
seq1 = alignlib.makeSequence( str(rep_seq) )
seq2 = alignlib.makeSequence( str(mem_seq) )
alignator.align( result, seq1, seq2 )
if options.loglevel >= 5:
options.stdlog.write( "# ali\n%s\n" % alignlib.AlignmentFormatExplicit( result, seq1, seq2 ) )
pidentity = 100 * alignlib.calculatePercentIdentity( result, seq1, seq2 )
num_gaps = result.getNumGaps()
if options.loglevel >= 4:
options.stdlog.write( "# processing: id=%s class=%s pid=%5.2f rep_cov=%i mem_cov=%i\n" %\
( mem_id, mem_quality, pidentity, rep_coverage, mem_coverage ) )
if pidentity >= options.min_identity:
keep = False
if rep_coverage < mem_coverage - options.safety_coverage or \
rep_pid < mem_pid - options.safety_pide:
keep = True
reason = "covpid"
elif num_gaps >= options.max_gaps and \
mem_coverage > rep_coverage - options.safety_coverage:
keep = True
reason = "gaps"
elif mem_coverage >= rep_coverage - options.safety_coverage and \
100 * (result.getColTo() - result.getColFrom()) / len(mem_seq) < options.max_member_coverage:
keep = True
reason = "memcov"
if keep:
options.stdlog.write( "# WARNING: not removing possibly good prediction: %s: rep = %s, mem = %s, rep_cov=%i, rep_pid=%i, mem_cov=%i, mem_pid=%i\n" %\
(reason, rep_id, mem_id, rep_coverage, rep_pid, mem_coverage, mem_pid) )
else:
eliminated_predictions[mem_id] = rep_id
eliminated.append( (mem_id, "h") )
elif pidentity >= options.min_identity_non_genes and \
this_quality in options.quality_genes and \
mem_quality not in options.quality_genes:
if rep_coverage < mem_coverage - options.safety_coverage or \
rep_pid < mem_pid - options.safety_pide:
options.stdlog.write( "# WARNING: not removing possibly good prediction: rep = %s, mem = %s, rep_cov=%i, rep_pid=%i, mem_cov=%i, mem_pid=%i\n" %\
(rep_id, mem_id, rep_coverage, rep_pid, mem_coverage, mem_pid) )
else:
eliminated_predictions[mem_id] = rep_id
eliminated.append( (mem_id, "l") )
return eliminated
if param_is_compressed:
if unaligned_pair and \
unaligned_pair.mToken1 == pair.mToken1 and \
unaligned_pair.mToken2 == pair.mToken2 and \
unaligned_pair.mIntronId1 == pair.mIntronId1:
map_a2b = alignlib.makeAlignmentVector()
f = AlignmentFormatEmissions(
pair.mFrom1,
pair.mAlignedSequence1,
pair.mFrom2,
pair.mAlignedSequence2).copy( map_a2b )
map_a2b.moveAlignment( -unaligned_pair.mFrom1 + 1, -unaligned_pair.mFrom2 + 1 )
data = alignlib.AlignmentFormatExplicit( map_a2b,
alignlib.makeSequence( unaligned_pair.mAlignedSequence1),
alignlib.makeSequence( unaligned_pair.mAlignedSequence2) )
from1, ali1, to1 = data.mRowFrom, data.mRowAlignment, data.mRowTo
from2, ali2, to2 = data.mColFrom, data.mColAlignment, data.mColTo
pair.mAlignedSequence1 = ali1
pair.mAlignedSequence2 = ali2
else:
raise "sequence not found for pair %s" % str(pair)
if param_do_gblocks:
if param_loglevel >= 4:
print "# length before: %i %i" % (len(pair.mAlignedSequence1), pair.mAligned)
print "# WARNING: discrepancy in exon calculation!!!"
for e in exons:
print "#", str(e)
print "#", str(entry)
if options.loglevel >= 5:
for e in exons:
print "#", str(e)
genomic_fragment = fasta.getSequence( entry.mSbjctToken, entry.mSbjctStrand,
entry.mSbjctGenomeFrom, entry.mSbjctGenomeTo )
skip = False
if peptide_sequences.has_key( entry.mQueryToken ):
query_sequence = alignlib.makeSequence(peptide_sequences[entry.mQueryToken])
sbjct_sequence = alignlib.makeSequence(entry.mTranslation)
percent_similarity, percent_identity = 0, 0
if query_sequence.getLength() < entry.mMapPeptide2Translation.getRowTo():
print "# WARNING: query sequence %s is too short: %i %i" % ( entry.mQueryToken,
query_sequence.getLength(),
entry.mMapPeptide2Translation.getRowTo())
sys.stdout.flush()
nmissed_length += 1
skip = True
elif sbjct_sequence.getLength() < entry.mMapPeptide2Translation.getColTo():
print "# WARNING: sbjct sequence %s is too short: %i %i" % ( entry.mSbjctToken,
sbjct_sequence.getLength(),
entry.mMapPeptide2Translation.getColTo())
old_length = mali.getLength()
new_mali = convertMali2Mali( mali )
if options.alignment_method == "sw":
alignator = alignlib.makeAlignatorFullDP( options.gop, options.gep )
else:
alignator = alignlib.makeAlignatorFullDPGlobal( options.gop, options.gep )
while 1:
cur_record = iterator.next()
if cur_record is None: break
map_mali2seq = alignlib.makeAlignataVector()
sequence = alignlib.makeSequence( cur_record.sequence )
profile = alignlib.makeProfileFromMali( new_mali )
if options.loglevel >= 4:
options.stdlog.write(profile.Write())
alignator.Align( profile, sequence, map_mali2seq )
if options.loglevel >= 3:
options.stdlog.write( map_mali2seq.Write() )
## add sequence to mali
a = alignlib.makeAlignatumFromString( cur_record.sequence )
a.thisown = 0
new_mali.addAlignatum( a, map_mali2seq, 1, 1, 1, 1, 1 )