def finish(self):
# Once executed, alignment is converted into relaxed
# interleaved phylip format.
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)
def finish(self):
# Once executed, alignment is converted into relaxed
# interleaved phylip format.
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)
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_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)
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)
