def realign_file(args, model, output_filename, alignment_filename):
# begin of HACK
if args.expand_model:
old_tracks = args.tracks
args.tracks.add('trf_cons')
m = model
if args.annotation_model:
m = args.annotation_model
annotations = compute_annotations(args, alignment_filename, m)
if args.expand_model:
consensuses = annotations['trf_cons']
args.tracks = old_tracks
if 'trf_cons' not in old_tracks:
del args.tracks['trf_cons']
# end of HACK
with Open(output_filename, 'w') as output_file_object:
for aln in Fasta.load(
alignment_filename,
args.alignment_regexp,
Alignment,
sequence_selectors=args.sequence_regexp):
if len(aln.sequences) < 2:
sys.stderr.write("ERROR: not enough sequences in file\n")
return 1
if len(args.draw) == 0:
drawer = brainwash(AlignmentCanvas)()
else:
drawer = AlignmentCanvas()
drawer.add_original_alignment(aln)
aln, unmask_repeats = args.mask_repeats(aln, annotations)
seq1, seq2 = tuple(map(Fasta.alnToSeq, aln.sequences[:2]))
perf.msg("Data loaded in {time} seconds.")
perf.replace()
if args.expand_model:
# Potrebujem zistit konsenzy
A = consensuses[aln.names[0]]
B = consensuses[aln.names[1]]
cons = list(A.union(B))
real_model = model.expandModel({'consensus': cons})
else:
real_model = model
realigner = args.algorithm()
realigner.setDrawer(drawer)
realigner.prepareData(seq1, aln.names[0], seq2, aln.names[1], aln,
real_model, annotations, args)
aln = realigner.realign(0, len(seq1), 0, len(seq2))
aln = unmask_repeats(aln)
perf.msg("Sequence was realigned in {time} seconds.")
perf.replace()
if len(args.draw) > 0:
drawer.add_sequence('X', seq1)
drawer.add_sequence('Y', seq2)
drawer.add_alignment_line(101, (255, 0, 255, 255), 2,
AlignmentPositionGenerator(
Alignment([aln[0], aln[2]])))
drawer.draw(args.draw, 2000, 2000)
perf.msg("Image was drawn in {time} seconds.")
# Save output_file
Fasta.saveAlignmentPiece(aln, output_file_object)
def compute_annotations(args, alignment_filename, model):
annotations = dict()
if 'trf' in args.tracks:
trf = None
for trf_executable in args.trf:
if os.path.exists(trf_executable):
trf = TRFDriver(trf_executable, mathType=args.mathType)
#break
if trf:
repeats = trf.run(alignment_filename)
annotations['trf'] = repeats
if 'original_repeats' in args.tracks:
repeats = json.load(Open(alignment_filename + '.repeats',
'r'))
for k, v in repeats.iteritems():
repeats[k] = [Repeat(_v[0], _v[1], _v[2], _v[3], _v[4])
for _v in v]
annotations['original_repeats'] = repeats
if 'trf_cons' in args.tracks:
trf = None
for trf_executable in args.trf:
if os.path.exists(trf_executable):
trf = TRFDriver(trf_executable, mathType=args.mathType)
#break
if trf:
repeats = trf.run(alignment_filename)
# repeats = json.load(Open(alignment_filename + '.repeats',
# 'r'))
# for k, v in repeats.iteritems():
# repeats[k] = [Repeat(_v[0], _v[1], _v[2], _v[3], _v[4])
# for _v in v]
annotations['trf_cons'] = {}
for seq_name in repeats:
cons = set([repeat.consensus for repeat in repeats[seq_name]])
annotations['trf_cons'][seq_name] = cons
if 'hmm' in args.tracks:
paths = None;
if args.trf != None and len(args.trf) > 0:
paths = args.trf
driver = HMMDriver(paths, args.mathType, model)
if driver:
repeats = driver.run(alignment_filename)
annotations['hmm'] = repeats
perf.msg("Hints computed in {time} seconds.")
perf.replace()
return annotations
def getTable(self, X, x, dx, Y, y, dy, tables,
forwardTable=None, backwardTable=None,
positionGenerator=None):
# Najskor chcem taku, co predpoklada ze obe tabulky su velke
# Potom chcem taku, ktora si bude doratavat chybajuce
# Potom pridat switch, ktory mi umozni robit optimalizacie.
# Ale potom bude treba vediet, ci ist od predu, alebo od zadu
# Fetch tables if they are not provided
if positionGenerator != None:
positionGenerator = list(positionGenerator)
perf.push()
forwardTable = jcpoint(
lambda:
forwardTable
if forwardTable != None else
self.getForwardTableGenerator(X, x, dx, Y, y, dy,
positionGenerator=positionGenerator),
'forward_table',
self.io_files,
self.mathType,
)
perf.msg('Forward table was computed in {time} seconds.')
perf.replace()
backwardTable = jcpoint(
lambda:
backwardTable
if backwardTable != None else
self.getBackwardTable(X, x, dx, Y, y, dy,
positionGenerator=positionGenerator),
'backward_table',
self.io_files,
self.mathType,
)
perf.msg('Backward table was computed in {time} seconds.')
perf.replace()
# Sort tables by first element (just in case)
sorted(backwardTable,key=lambda (x,_) : x)
perf.msg('Tables were sorted in {time} seconds.')
perf.replace()
# Convert forward table into list
#ft = [dict() for _ in range(dx + 1)]
#for (i, _x) in forwardTable:
# ft[i - x] = _x
# Convert backward table into list
bt = [dict() for _ in range(dx + 1)]
for (i, B) in backwardTable:
bt[i] = B
perf.msg('Backward table was flattened in {time} seconds.')
perf.replace()
States = [table(dx, self) for table in tables]
index = 0
for i, row in forwardTable:
#slice position generator
while (index < len(positionGenerator) and
positionGenerator[index][0] < i):
index += 1
start = index
while (index < len(positionGenerator) and
positionGenerator[index][0] <= i):
index += 1
for table in States:
table.processRow(X, x, dx, Y, y, dy, i, row, bt,
positionGenerator[start:index])
ret = [table.getData() for table in States]
# ret = [table(X, x, dx, Y, y, dy, ft, bt, positionGenerator)
# for table in tables]
perf.msg('Posterior table was computed in {time} seconds.')
perf.pop()
return ret
def getTable(self,
X,
x,
dx,
Y,
y,
dy,
tables,
forwardTable=None,
backwardTable=None,
positionGenerator=None):
# Najskor chcem taku, co predpoklada ze obe tabulky su velke
# Potom chcem taku, ktora si bude doratavat chybajuce
# Potom pridat switch, ktory mi umozni robit optimalizacie.
# Ale potom bude treba vediet, ci ist od predu, alebo od zadu
# Fetch tables if they are not provided
if positionGenerator != None:
positionGenerator = list(positionGenerator)
perf.push()
forwardTable = jcpoint(
lambda: forwardTable
if forwardTable != None else self.getForwardTableGenerator(
X, x, dx, Y, y, dy, positionGenerator=positionGenerator),
'forward_table',
self.io_files,
self.mathType,
)
perf.msg('Forward table was computed in {time} seconds.')
perf.replace()
backwardTable = jcpoint(
lambda: backwardTable
if backwardTable != None else self.getBackwardTable(
X, x, dx, Y, y, dy, positionGenerator=positionGenerator),
'backward_table',
self.io_files,
self.mathType,
)
perf.msg('Backward table was computed in {time} seconds.')
perf.replace()
# Sort tables by first element (just in case)
sorted(backwardTable, key=lambda (x, _): x)
perf.msg('Tables were sorted in {time} seconds.')
perf.replace()
# Convert forward table into list
#ft = [dict() for _ in range(dx + 1)]
#for (i, _x) in forwardTable:
# ft[i - x] = _x
# Convert backward table into list
bt = [dict() for _ in range(dx + 1)]
for (i, B) in backwardTable:
bt[i] = B
perf.msg('Backward table was flattened in {time} seconds.')
perf.replace()
States = [table(dx, self) for table in tables]
index = 0
for i, row in forwardTable:
#slice position generator
while (index < len(positionGenerator)
and positionGenerator[index][0] < i):
index += 1
start = index
while (index < len(positionGenerator)
and positionGenerator[index][0] <= i):
index += 1
for table in States:
table.processRow(X, x, dx, Y, y, dy, i, row, bt,
positionGenerator[start:index])
ret = [table.getData() for table in States]
# ret = [table(X, x, dx, Y, y, dy, ft, bt, positionGenerator)
# for table in tables]
perf.msg('Posterior table was computed in {time} seconds.')
perf.pop()
return ret
