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. Both files, fasta and phylip,
# remain accessible.
# Set Task specific attributes
main_job = self.jobs[0]
fasta_path = pjoin(main_job.jobdir, "clean.alg.fasta")
alg = SeqGroup(fasta_path)
if len(alg) != self.size:
log.warning(
"Trimming was to aggressive and it tried"
" to remove one or more sequences."
" Alignment trimming will be disabled for this dataset.")
self.clean_alg_fasta_file = db.register_task_data(
self.taskid, DATATYPES.clean_alg_fasta, self.alg_fasta_file)
self.clean_alg_phylip_file = db.register_task_data(
self.taskid, DATATYPES.clean_alg_phylip, self.alg_phylip_file)
else:
for line in open(self.jobs[0].stdout_file):
line = line.strip()
if line.startswith("#ColumnsMap"):
kept_columns = list(
map(int,
line.split("\t")[1].split(",")))
fasta = alg.write(format="fasta")
phylip = alg.write(format="iphylip_relaxed")
AlgCleanerTask.store_data(self, fasta, phylip, kept_columns)
def finish(self):
# Once executed, alignment is converted into relaxed
# interleaved phylip format.
final_job = self.jobs[2]
alg = SeqGroup(os.path.join(final_job.jobdir, "alg.fasta"))
alg.write(outfile=self.alg_fasta_file, format="fasta")
alg.write(outfile=self.alg_phylip_file, format="iphylip_relaxed")
AlgTask.finish(self)
def finish(self):
# Once executed, alignment is converted into relaxed
# interleaved phylip format.
final_job = self.jobs[2]
alg = SeqGroup(os.path.join(final_job.jobdir, "alg.fasta"))
alg.write(outfile=self.alg_fasta_file, format="fasta")
alg.write(outfile=self.alg_phylip_file, format="iphylip_relaxed")
AlgTask.finish(self)
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):
# Once executed, alignment is converted into relaxed
# interleaved phylip format. Both files, fasta and phylip,
# remain accessible.
# Set Task specific attributes
main_job = self.jobs[0]
fasta_path = pjoin(main_job.jobdir, "clean.alg.fasta")
alg = SeqGroup(fasta_path)
if len(alg) != self.size:
log.warning("Trimming was to aggressive and it tried"
" to remove one or more sequences."
" Alignment trimming will be disabled for this dataset."
)
self.clean_alg_fasta_file = db.register_task_data(self.taskid, DATATYPES.clean_alg_fasta, self.alg_fasta_file)
self.clean_alg_phylip_file = db.register_task_data(self.taskid, DATATYPES.clean_alg_phylip, self.alg_phylip_file)
else:
for line in open(self.jobs[0].stdout_file):
line = line.strip()
if line.startswith("#ColumnsMap"):
kept_columns = list(map(int, line.split("\t")[1].split(",")))
fasta = alg.write(format="fasta")
phylip = alg.write(format="iphylip_relaxed")
AlgCleanerTask.store_data(self, fasta, phylip, kept_columns)
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)