def _bootstrap(self, rep_num):
"""Infer tree from bootstrapped multiple sequence alignment.
Parameters
----------
replicated_num : int
Unique replicate number.
cpus : int
Number of cpus to use.
"""
rep_dir = os.path.join(self.output_dir, 'rep_%d' % rep_num)
if not os.path.exists(rep_dir):
os.makedirs(rep_dir)
output_msa = os.path.join(rep_dir, 'bootstrap.afa')
bootstrap_alignment(self.msa, output_msa)
phylip_msa_file = output_msa.replace('.afa', '.phyx')
cmd = 'seqmagick convert %s %s' % (output_msa, phylip_msa_file)
os.system(cmd)
log_file = os.path.join(rep_dir, 'raxml.log')
self.run(phylip_msa_file, self.model, rep_dir, log_file, output_suffix='support')
return True
def _producer(self, replicated_num):
"""Infer tree from bootstrapped multiple sequence alignment.
Parameters
----------
replicated_num : int
Unique replicate number.
"""
output_msa = os.path.join(
self.replicate_dir,
'bootstrap_msa.r_' + str(replicated_num) + '.fna')
if os.path.exists(output_msa) and os.path.getsize(output_msa) > 0:
self.logger.warning(
'Skipping {} as it already exists.'.format(output_msa))
return True
output_tree = os.path.join(
self.replicate_dir,
'bootstrap_tree.r_' + str(replicated_num) + '.tree')
fast_tree_output = os.path.join(
self.replicate_dir,
'bootstrap_fasttree.r_' + str(replicated_num) + '.out')
if os.path.exists(
fast_tree_output) and os.path.getsize(fast_tree_output) > 0:
self.logger.warning(
'Skipping {} as it already exists.'.format(fast_tree_output))
return True
bootstrap_alignment(self.msa, output_msa, frac=self.frac)
fast_tree = FastTree(multithreaded=False)
cmd = fast_tree.run(output_msa, self.base_type, self.model, self.gamma,
output_tree, fast_tree_output)
return True
def _producer(self, replicated_num):
"""Infer tree from bootstrapped multiple sequence alignment.
Parameters
----------
replicated_num : int
Unique replicate number.
"""
output_msa = os.path.join(
self.replicate_dir,
'bootstrap_msa.r_' + str(replicated_num) + '.fna')
bootstrap_alignment(self.msa, output_msa, frac=self.frac)
fast_tree = FastTree(multithreaded=False)
output_tree = os.path.join(
self.replicate_dir,
'bootstrap_tree.r_' + str(replicated_num) + '.tree')
fast_tree_output = os.path.join(
self.replicate_dir,
'bootstrap_fasttree.r_' + str(replicated_num) + '.out')
fast_tree.run(output_msa, self.base_type, self.model, output_tree,
fast_tree_output)
return True
def _producer(self, replicated_num):
"""Infer tree from bootstrapped multiple sequence alignment.
Parameters
----------
replicated_num : int
Unique replicate number.
"""
output_msa = os.path.join(self.replicate_dir, 'bootstrap_msa.r_' + str(replicated_num) + '.fna')
bootstrap_alignment(self.msa, output_msa, frac=self.frac)
fast_tree = FastTree(multithreaded=False)
output_tree = os.path.join(self.replicate_dir, 'bootstrap_tree.r_' + str(replicated_num) + '.tree')
fast_tree_output = os.path.join(self.replicate_dir, 'bootstrap_fasttree.r_' + str(replicated_num) + '.out')
fast_tree.run(output_msa, self.base_type, self.model, self.gamma, output_tree, fast_tree_output)
return True
def _bootstrap(self, replicated_num):
"""Infer tree from bootstrapped multiple sequence alignment.
Parameters
----------
replicated_num : int
Unique replicate number.
cpus : int
Number of cpus to use.
"""
output_msa = os.path.join(self.replicate_dir, 'bootstrap.msa.' + str(replicated_num) + '.fna')
bootstrap_alignment(self.msa, output_msa)
output_tree = os.path.join(self.replicate_dir, 'bootstrap.tree.' + str(replicated_num) + '.tre')
fast_tree_output = os.path.join(self.replicate_dir, 'bootstrap.fasttree.' + str(replicated_num) + '.out')
self.run(output_msa, self.seq_type, self.model, output_tree, fast_tree_output)
return True
def _bootstrap(self, rep_num):
"""Infer tree from bootstrapped multiple sequence alignment.
Parameters
----------
replicated_num : int
Unique replicate number.
cpus : int
Number of cpus to use.
"""
rep_dir = os.path.join(self.output_dir, 'rep_%d' % rep_num)
if not os.path.exists(rep_dir):
os.makedirs(rep_dir)
output_msa = os.path.join(rep_dir, 'bootstrap.afa')
bootstrap_alignment(self.msa, output_msa)
output_tree = os.path.join(rep_dir, 'bootstrap.tree')
log_file = os.path.join(rep_dir, 'fasttree.log')
self.run(output_msa, self.seq_type, self.model, output_tree, log_file)
return True
