def build_jobs(self):
assert isinstance(self.root_problem, SeppProblem)
for placement_problem in self.root_problem.get_children():
''' Create placer jobs'''
if self.placer == "pplacer":
pj = PplacerJob()
pj.partial_setup_for_subproblem(placement_problem, self.options.info_file)
elif self.placer == "epa":
pj = EPAJob()
pj.partial_setup_for_subproblem(placement_problem, self.molecule)
placement_problem.add_job("placer",pj)
'''For each alignment subproblem, ...'''
for alg_problem in placement_problem.children:
assert isinstance(alg_problem, SeppProblem)
''' create the build model job'''
bj = HMMBuildJob()
bj.setup_for_subproblem(alg_problem,molecule=self.molecule)
alg_problem.add_job(bj.job_type, bj)
''' create the search jobs'''
for fc_problem in alg_problem.get_children():
sj = HMMSearchJob()
sj.partial_setup_for_subproblem(fc_problem.fragments, fc_problem, self.elim, self.filters)
fc_problem.add_job(sj.job_type, sj)
''' create the align job'''
aj = HMMAlignJob()
fc_problem.add_job(aj.job_type, aj)
aj.partial_setup_for_subproblem(fc_problem, molecule=self.molecule)
def build_jobs(self):
assert isinstance(self.root_problem, SeppProblem)
for placement_problem in self.root_problem.get_children():
''' Create placer jobs'''
for i in range(0, self.root_problem.fragment_chunks):
pj = PplacerJob()
pj.partial_setup_for_subproblem(placement_problem,
self.options.info_file, i)
placement_problem.add_job(get_placement_job_name(i), pj)
'''For each alignment subproblem, ...'''
for alg_problem in placement_problem.children:
assert isinstance(alg_problem, SeppProblem)
''' create the build model job'''
bj = HMMBuildJob()
bj.setup_for_subproblem(alg_problem,
symfrac=self.symfrac,
molecule=self.molecule,
**vars(self.options.hmmbuild))
alg_problem.add_job(bj.job_type, bj)
''' create the search jobs'''
for fc_problem in alg_problem.get_children():
sj = HMMSearchJob()
sj.partial_setup_for_subproblem(fc_problem.fragments,
fc_problem, self.elim,
self.filters)
fc_problem.add_job(sj.job_type, sj)
''' create the align job'''
aj = HMMAlignJob()
fc_problem.add_job(aj.job_type, aj)
aj.partial_setup_for_subproblem(fc_problem,
molecule=self.molecule)
def build_jobs(self):
assert isinstance(self.root_problem, SeppProblem)
for placement_problem in self.root_problem.get_children():
''' Create placer jobs'''
if self.placer == "pplacer":
pj = PplacerJob()
pj.partial_setup_for_subproblem(placement_problem,
self.options.info_file)
elif self.placer == "epa":
pj = EPAJob()
pj.partial_setup_for_subproblem(placement_problem,
self.molecule)
placement_problem.add_job("placer", pj)
'''For each alignment subproblem, ...'''
for alg_problem in placement_problem.children:
assert isinstance(alg_problem, SeppProblem)
''' create the build model job'''
bj = HMMBuildJob()
bj.setup_for_subproblem(alg_problem, molecule=self.molecule)
alg_problem.add_job(bj.job_type, bj)
''' create the search jobs'''
for fc_problem in alg_problem.get_children():
sj = HMMSearchJob()
sj.partial_setup_for_subproblem(fc_problem.fragments,
fc_problem, self.elim,
self.filters)
fc_problem.add_job(sj.job_type, sj)
''' create the align job'''
aj = HMMAlignJob()
fc_problem.add_job(aj.job_type, aj)
aj.partial_setup_for_subproblem(fc_problem,
molecule=self.molecule)
def build_jobs(self):
assert isinstance(self.root_problem, SeppProblem)
for placement_problem in self.root_problem.get_children():
''' Create placer jobs'''
for i in range(0, self.root_problem.fragment_chunks):
if self.placer == "pplacer":
pj = PplacerJob()
pj.partial_setup_for_subproblem(placement_problem,
self.options.info_file, i)
elif self.placer == "epa":
raise ValueError("EPA Currently not supported")
# pj = EPAJob()
# pj.partial_setup_for_subproblem(
# placement_problem, self.molecule, i)
placement_problem.add_job(get_placement_job_name(i), pj)
'''For each alignment subproblem, ...'''
for alg_problem in placement_problem.children:
assert isinstance(alg_problem, SeppProblem)
''' create the build model job'''
bj = HMMBuildJob()
bj.setup_for_subproblem(alg_problem, molecule=self.molecule)
alg_problem.add_job(bj.job_type, bj)
''' create the search jobs'''
for fc_problem in alg_problem.get_children():
sj = HMMSearchJob()
sj.partial_setup_for_subproblem(fc_problem.fragments,
fc_problem, self.elim,
self.filters)
fc_problem.add_job(sj.job_type, sj)
''' create the align job'''
aj = HMMAlignJob()
fc_problem.add_job(aj.job_type, aj)
aj.partial_setup_for_subproblem(fc_problem,
molecule=self.molecule)
def build_jobs(self):
assert isinstance(self.root_problem, SeppProblem)
for placement_problem in self.root_problem.get_children():
""" Create pplacer jobs"""
pj = PplacerJob()
placement_problem.add_job(pj.job_type, pj)
pj.partial_setup_for_subproblem(placement_problem, self.options.info_file)
"""For each alignment subproblem, ..."""
for alg_problem in placement_problem.children:
assert isinstance(alg_problem, SeppProblem)
""" create the build model job"""
bj = HMMBuildJob()
# pdb.set_trace()
bj.setup_for_subproblem(
alg_problem, symfrac=self.symfrac, molecule=self.molecule, **vars(self.options.hmmbuild)
)
alg_problem.add_job(bj.job_type, bj)
""" create the search jobs"""
for fc_problem in alg_problem.get_children():
sj = HMMSearchJob()
sj.partial_setup_for_subproblem(fc_problem.fragments, fc_problem, self.elim, self.filters)
fc_problem.add_job(sj.job_type, sj)
""" create the align job"""
aj = HMMAlignJob()
fc_problem.add_job(aj.job_type, aj)
aj.partial_setup_for_subproblem(fc_problem, molecule=self.molecule)
def build_jobs(self):
assert isinstance(self.root_problem, SeppProblem)
for placement_problem in self.root_problem.get_children():
''' Create placer jobs'''
for i in range(0, self.root_problem.fragment_chunks):
pj = PplacerJob()
pj.partial_setup_for_subproblem(
placement_problem, self.options.info_file, i)
placement_problem.add_job(get_placement_job_name(i), pj)
'''For each alignment subproblem, ...'''
for alg_problem in placement_problem.children:
assert isinstance(alg_problem, SeppProblem)
''' create the build model job'''
bj = HMMBuildJob()
bj.setup_for_subproblem(
alg_problem, symfrac=self.symfrac,
molecule=self.molecule,
**vars(self.options.hmmbuild))
alg_problem.add_job(bj.job_type, bj)
''' create the search jobs'''
for fc_problem in alg_problem.get_children():
sj = HMMSearchJob()
sj.partial_setup_for_subproblem(
fc_problem.fragments,
fc_problem, self.elim, self.filters)
fc_problem.add_job(sj.job_type, sj)
''' create the align job'''
aj = HMMAlignJob()
fc_problem.add_job(aj.job_type, aj)
aj.partial_setup_for_subproblem(
fc_problem, molecule=self.molecule)
def build_jobs(self):
assert isinstance(self.root_problem, SeppProblem)
for placement_problem in self.root_problem.get_children():
''' Create placer jobs'''
for i in range(0, self.root_problem.fragment_chunks):
if self.placer == "pplacer":
pj = PplacerJob()
pj.partial_setup_for_subproblem(
placement_problem, self.options.info_file, i)
elif self.placer == "epa":
raise ValueError("EPA Currently not supported")
# pj = EPAJob()
# pj.partial_setup_for_subproblem(
# placement_problem, self.molecule, i)
placement_problem.add_job(get_placement_job_name(i), pj)
'''For each alignment subproblem, ...'''
for alg_problem in placement_problem.children:
assert isinstance(alg_problem, SeppProblem)
''' create the build model job'''
bj = HMMBuildJob()
bj.setup_for_subproblem(alg_problem, molecule=self.molecule)
alg_problem.add_job(bj.job_type, bj)
''' create the search jobs'''
for fc_problem in alg_problem.get_children():
sj = HMMSearchJob()
sj.partial_setup_for_subproblem(
fc_problem.fragments, fc_problem, self.elim,
self.filters)
fc_problem.add_job(sj.job_type, sj)
''' create the align job'''
aj = HMMAlignJob()
fc_problem.add_job(aj.job_type, aj)
aj.partial_setup_for_subproblem(
fc_problem, molecule=self.molecule)