def create_job(self,
alignment,
starting_tree=None,
name='default',
**kwargs):
scratch_dir, seqfn, dt, score_fn = self._prepare_input(
alignment, **kwargs)
invoc = [
sys.executable,
self.exe,
seqfn,
dt,
os.path.join(scratch_dir, 'output.tre'),
]
dirs_to_delete = []
if kwargs.get('delete_temps', self.delete_temps):
dirs_to_delete.append(scratch_dir)
pasta_products = kwargs.get('pasta_products')
step_num = kwargs.get('step_num')
def randtree_result_processor(dir=scratch_dir,
score_fn=score_fn,
fn=os.path.join(scratch_dir,
'output.tre'),
dirs_to_delete=dirs_to_delete,
temp_fs=self.temp_fs,
pasta_products=pasta_products,
step_num=step_num):
score = float(open(score_fn, 'rU').read().strip())
tree_str = open(fn, 'rU').read().strip()
copy_temp_tree(fn, pasta_products, step_num)
for d in dirs_to_delete:
temp_fs.remove_dir(d)
return (score, tree_str)
job_id = kwargs.get('context_str', '') + '_randtree'
job = DispatchableJob(invoc,
result_processor=randtree_result_processor,
cwd=scratch_dir,
context_str=job_id,
stdout=score_fn)
return job
def create_job(self, alignment, starting_tree=None, **kwargs):
scratch_dir, seqfn, datatype, options = self._prepare_input(
alignment, **kwargs)
num_cpus = kwargs.get('num_cpus')
log_file = os.path.join(scratch_dir, 'log')
invoc = [self.exe, '-quiet']
if datatype != '':
invoc.extend([datatype])
model = self.model if self.model is not None else ''
if model != '':
model = model.split(' ')
invoc.extend(model)
#elif datatype == '-nt':
# model = '-gtr'
# invoc.append(model)
if options is not None and len(options) >= 1:
invoc.extend(options)
fasttree_result = os.path.join(scratch_dir, 'results')
if starting_tree is not None:
if isinstance(starting_tree, str):
tree_str = starting_tree
else:
tree_str = str(starting_tree)
tree_fn = os.path.join(os.path.abspath(scratch_dir), "start.tre")
tree_file_obj = open(tree_fn, "w")
tree_file_obj.write("%s;\n" % tree_str)
tree_file_obj.close()
invoc.extend(['-intree', tree_fn])
invoc.extend(['-log', log_file, seqfn])
if num_cpus > 1:
if platform.system() == 'Windows':
mp_path = self.exe.replace('.', 'MP.')
else:
mp_path = self.exe + 'MP'
if os.path.exists(mp_path):
os.environ["OMP_NUM_THREADS"] = str(
num_cpus if num_cpus < 5 else 4)
invoc[0] = mp_path
dirs_to_delete = []
if kwargs.get('delete_temps', self.delete_temps):
dirs_to_delete.append(scratch_dir)
pasta_products = kwargs.get('pasta_products')
step_num = kwargs.get('step_num')
rpc = lambda: read_fasttree_results(
scratch_dir,
fasttree_result,
log_file,
delete_dir=kwargs.get('delete_temps', self.delete_temps),
pasta_products=pasta_products,
step_num=step_num)
job_id = kwargs.get('context_str', '') + '_fasttree'
job = DispatchableJob(invoc,
result_processor=rpc,
cwd=scratch_dir,
stdout=fasttree_result,
context_str=job_id)
return job
def create_job(self,
alignment,
starting_tree=None,
name='default',
**kwargs):
scratch_dir, seqfn, parfn, model = self._prepare_input(
alignment, **kwargs)
num_cpus = kwargs.get('num_cpus')
invoc = [
self.exe,
'-m',
model,
'-n',
name,
'-q',
parfn,
'-s',
seqfn,
# '-M', # Branch length estimates per partition
]
#x = open(parfn).readlines()
#npar = [i.count(',') for i in x]
# if npar > 1:
# invoc.extend('-M')
if self.user_opts is not None and len(self.user_opts) >= 1:
invoc.extend(self.user_opts)
if starting_tree is not None:
if isinstance(starting_tree, str):
tree_str = starting_tree
else:
tree_str = str(starting_tree)
tree_fn = os.path.join(os.path.abspath(scratch_dir), "start.tre")
tree_file_obj = open(tree_fn, "w")
tree_file_obj.write("%s;\n" % tree_str)
tree_file_obj.close()
invoc.extend(['-t', tree_fn])
if num_cpus > 1:
invoc.extend(['-T', str(num_cpus)])
if platform.system() == 'Windows':
x = invoc[0].split('.')
x[-2] += 'p'
invoc[0] = '.'.join(x)
else:
invoc[0] += 'p'
if GLOBAL_DEBUG:
invoc.extend(['-p', '123456789'])
dirs_to_delete = []
if kwargs.get('delete_temps', self.delete_temps):
dirs_to_delete.append(scratch_dir)
pasta_products = kwargs.get('pasta_products')
step_num = kwargs.get('step_num')
rpc = lambda: read_raxml_results(scratch_dir,
dirs_to_delete=dirs_to_delete,
temp_fs=self.temp_fs,
pasta_products=pasta_products,
step_num=step_num)
job_id = kwargs.get('context_str', '') + '_raxml'
job = DispatchableJob(invoc,
result_processor=rpc,
cwd=scratch_dir,
context_str=job_id)
return job