def finish(self): # Once executed, alignment is converted into relaxed # interleaved phylip format. alg = SeqGroup(self.jobs[0].stdout_file) fasta = alg.write(format="fasta") phylip = alg.write(format="iphylip_relaxed") AlgTask.store_data(self, fasta, phylip)
def finish(self): # Once executed, alignment is converted into relaxed # interleaved phylip format. alg_file = os.path.join(self.jobs[0].jobdir, "alg.fasta") # ClustalO returns a tricky fasta file alg = read_fasta(alg_file, header_delimiter=" ") fasta = alg.write(format="fasta") phylip = alg.write(format="iphylip_relaxed") AlgTask.store_data(self, fasta, phylip)
def finish(self): # Once executed, alignment is converted into relaxed # interleaved phylip format. alg = SeqGroup(os.path.join(self.jobs[0].jobdir, "mcoffee.fasta")) fasta = alg.write(format="fasta") phylip = alg.write(format="iphylip_relaxed") alg_list_string = '\n'.join([pjoin(GLOBALS["input_dir"], aname) for aname in self.all_alg_files]) db.add_task_data(self.taskid, DATATYPES.alg_list, alg_list_string) AlgTask.store_data(self, fasta, phylip)
def finish(self): if self.conf[self.confname]["_alg_trimming"]: # If trimming happened after mcoffee, let's save the # resulting output trim_job = self.jobs[-1] alg = SeqGroup(pjoin(trim_job.jobdir, trim_job.alg_fasta_file)) fasta = alg.write(format="fasta") phylip = alg.write(format="iphylip_relaxed") AlgTask.store_data(self, fasta, phylip) else: # If no post trimming, output is just what Mcoffee # produced, so we can recycle its data ids. mc_task = self.jobs[-1] fasta_id = db.get_dataid(mc_task.taskid, DATATYPES.alg_fasta) phylip_id = db.get_dataid(mc_task.taskid, DATATYPES.alg_phylip) db.register_task_data(self.taskid, DATATYPES.alg_fasta, fasta_id) db.register_task_data(self.taskid, DATATYPES.alg_phylip, phylip_id)
def finish(self): alg = SeqGroup(os.path.join(self.jobs[0].jobdir, "alg.fasta")) fasta = alg.write(format="fasta") phylip = alg.write(format="iphylip_relaxed") AlgTask.store_data(self, fasta, phylip)