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)
示例#2
0
 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)
示例#3
0
    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)
示例#4
0
    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)
示例#5
0
    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)
示例#6
0
    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)
示例#7
0
    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)