def load_jobs(self):
readal_bin = self.conf["app"]["readal"]
trimal_bin = self.conf["app"]["trimal"]
input_dir = GLOBALS["input_dir"]
multiseq_file = pjoin(input_dir, self.multiseq_file)
multiseq_file_r = pjoin(input_dir, self.multiseq_file+"_reversed")
first = seq_reverser_job(multiseq_file, multiseq_file_r,
[self.nodeid], readal_bin)
#print self.multiseq_file
first.add_input_file(self.multiseq_file)
self.jobs.append(first)
all_alg_names = []
mcoffee_parents = []
for aligner_name in self.conf[self.confname]["_aligners"]:
aligner_name = aligner_name[1:]
_classname = APP2CLASS[self.conf[aligner_name]["_app"]]
_module = __import__(CLASS2MODULE[_classname], globals(), locals(), [], -1)
_aligner = getattr(_module, _classname)
# Normal alg
task1 = _aligner(self.nodeid, self.multiseq_file, self.seqtype,
self.conf, aligner_name)
task1.size = self.size
self.jobs.append(task1)
all_alg_names.append(task1.alg_fasta_file)
# Alg of the reverse
task2 = _aligner(self.nodeid, self.multiseq_file+"_reversed",
self.seqtype, self.conf, aligner_name)
task2.size = self.size
task2.dependencies.add(first)
self.jobs.append(task2)
# Restore reverse alg
reverse_out = pjoin(input_dir, task2.alg_fasta_file)
task3 = seq_reverser_job(reverse_out,
reverse_out+"_restored",
[task2.taskid], readal_bin)
task3.dependencies.add(task2)
task3.add_input_file(task2.alg_fasta_file)
all_alg_names.append(reverse_out+"_restored")
self.jobs.append(task3)
mcoffee_parents.extend([task1.taskid, task2.taskid])
# Combine signal from all algs using Mcoffee
mcoffee_task = MCoffee(self.nodeid, self.seqtype, all_alg_names,
self.conf, self.confname, parent_ids=mcoffee_parents)
# reversed algs are not actually saved into db, but it should
# be present since the reverser job is always executed
mcoffee_task.dependencies.update(list(self.jobs))
self.jobs.append(mcoffee_task)
if self.conf[self.confname]["_alg_trimming"]:
trimming_cutoff = 1.0 / len(all_alg_names)
targs = {}
targs["-forceselect"] = pjoin(input_dir, mcoffee_task.alg_fasta_file)
targs["-compareset"] = pjoin(input_dir, mcoffee_task.alg_list_file)
targs["-out"] = "mcoffee.trimmed.fasta"
targs["-fasta"] = ""
targs["-ct"] = trimming_cutoff
trim_job = Job(trimal_bin, targs, parent_ids=[mcoffee_task.taskid])
trim_job.jobname = "McoffeeTrimming"
trim_job.dependencies.add(mcoffee_task)
trim_job.alg_fasta_file = targs["-out"]
for key in all_alg_names:
trim_job.add_input_file(key)
trim_job.add_input_file(mcoffee_task.alg_fasta_file)
trim_job.add_input_file(mcoffee_task.alg_list_file)
self.jobs.append(trim_job)
