def _seed(self, trys):
"""BLAST seedsize sequences together, align and return True
if successful"""
self.minlen = min([self.seqstore[e][1] for e in self.seqstore.keys()])
sequences = self.seqstore.start(self.seedsize)
# make sure there are enough seqs for alignment
if len(sequences) >= self.minseedsize:
command = version(sequences, self.type)
try:
alignment, seconds = timeit(
func=align,
command=command,
sequences=sequences,
logger=self.logger,
wd=self.wd,
threads=self.threads,
timeout=self._getTimeout(sequences),
)
except MafftError:
self.logger.debug("MAFTT error raised")
success = False
else:
success = self._check(alignment)
else:
success = False
# add to trys if unsuccessful or sequences are fewer than
# seedsize
trys += self._calcSeedsize(success and len(sequences) == self.seedsize)
if success:
self._calcTimeout(seconds, alignment)
self.store.append(alignment)
return success, trys
def _seed(self, trys):
"""BLAST seedsize sequences together, align and return True
if successful"""
self.minlen = min([self.seqstore[e][1] for e in self.seqstore.keys()])
sequences = self.seqstore.start(self.seedsize)
# make sure there are enough seqs for alignment
if len(sequences) >= self.minseedsize:
command = version(sequences, self.type)
try:
alignment, seconds = timeit(
func=align,
command=command,
sequences=sequences,
logger=self.logger,
wd=self.wd,
threads=self.threads,
timeout=self._getTimeout(sequences))
except MafftError:
self.logger.debug('MAFTT error raised')
success = False
else:
success = self._check(alignment)
else:
success = False
# add to trys if unsuccessful or sequences are fewer than
# seedsize
trys += self._calcSeedsize(success and len(sequences) == self.seedsize)
if success:
self._calcTimeout(seconds, alignment)
self.store.append(alignment)
return success, trys
def _add(self, trys, limit=None):
"""Add sequence to alignment, return True if successful"""
alignment = self.store[-1]
self.minlen = min([self.seqstore[e][1] for e in self.seqstore.keys()])
if len(self.seqstore.sppool) == 0:
return True, trys
else:
sequence = self.seqstore.next(alignment, limit=limit)
if not sequence:
# if no sequence is returned, nothing more can be
# added
self.logger.debug("No new sequence added")
return True, trys
try:
new_alignment, seconds = timeit(
func=add,
alignment=alignment,
sequence=sequence,
logger=self.logger,
wd=self.wd,
threads=self.threads,
timeout=self._getTimeout(alignment, sequence),
)
except MafftError:
self.logger.debug("MAFFT error raised")
success = False
else:
success = self._check(new_alignment)
if success:
self._calcTimeout(seconds, alignment, align=False)
self.store.append(new_alignment)
else:
trys += 1
sequence = self.seqstore.back(alignment)
if not sequence:
# here a species has been dropped and now all
# species are present
return True, trys
return False, trys
def _add(self, trys, limit=None):
"""Add sequence to alignment, return True if successful"""
alignment = self.store[-1]
self.minlen = min([self.seqstore[e][1] for e in self.seqstore.keys()])
if len(self.seqstore.sppool) == 0:
return True, trys
else:
sequence = self.seqstore.next(alignment, limit=limit)
if not sequence:
# if no sequence is returned, nothing more can be
# added
self.logger.debug('No new sequence added')
return True, trys
try:
new_alignment, seconds = timeit(func=add,
alignment=alignment,
sequence=sequence,
logger=self.logger,
wd=self.wd,
threads=self.threads,
timeout=self._getTimeout(
alignment, sequence))
except MafftError:
self.logger.debug('MAFFT error raised')
success = False
else:
success = self._check(new_alignment)
if success:
self._calcTimeout(seconds, alignment, align=False)
self.store.append(new_alignment)
else:
trys += 1
sequence = self.seqstore.back(alignment)
if not sequence:
# here a species has been dropped and now all
# species are present
return True, trys
return False, trys
