def load_jobs(self):
appname = self.conf[self.confname]["_app"]
# Only one Muscle job is necessary to run this task
args = OrderedDict(self.args)
args["-i"] = pjoin(GLOBALS["input_dir"], self.multiseq_file)
args["-o"] = "alg.fasta"
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.cores = self.conf["threading"].get(appname, 1)
job.add_input_file(self.multiseq_file)
self.jobs.append(job)
def load_jobs(self):
appname = self.conf[self.confname]["_app"]
# Only one Muscle job is necessary to run this task
args = OrderedDict(self.args)
args["-i"] = pjoin(GLOBALS["input_dir"], self.multiseq_file)
args["-o"] = "alg.fasta"
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.cores = self.conf["threading"].get(appname, 1)
job.add_input_file(self.multiseq_file)
self.jobs.append(job)
def load_jobs(self):
appname = self.conf[self.confname]["_app"]
args = OrderedDict(self.args)
# Mafft redirects resulting alg to std.output. The order of
# arguments is important, input file must be the last
# one.
args[""] = pjoin(GLOBALS["input_dir"], self.multiseq_file)
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.add_input_file(self.multiseq_file)
job.cores = self.conf["threading"][appname]
self.jobs.append(job)
def load_jobs(self):
appname = self.conf[self.confname]["_app"]
args = OrderedDict(self.args)
# Mafft redirects resulting alg to std.output. The order of
# arguments is important, input file must be the last
# one.
args[""] = pjoin(GLOBALS["input_dir"], self.multiseq_file)
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.add_input_file(self.multiseq_file)
job.cores = self.conf["threading"][appname]
self.jobs.append(job)
def load_jobs(self):
args = self.args.copy()
try:
del args["-wag"]
except KeyError:
pass
if self.constrain_tree:
args["-constraints"] = pjoin(GLOBALS["input_dir"], self.constrain_tree)
args[pjoin(GLOBALS["input_dir"], self.alg_phylip_file)] = ""
appname = self.conf[self.confname]["_app"]
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.cores = self.conf["threading"][appname]
if self.constrain_tree:
job.add_input_file(self.constrain_tree)
job.add_input_file(self.alg_phylip_file)
self.jobs.append(job)
def load_jobs(self):
args = self.args.copy()
try:
del args["-wag"]
except KeyError:
pass
if self.constrain_tree:
args["-constraints"] = pjoin(GLOBALS["input_dir"],
self.constrain_tree)
args[pjoin(GLOBALS["input_dir"], self.alg_phylip_file)] = ""
appname = self.conf[self.confname]["_app"]
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.cores = self.conf["threading"][appname]
if self.constrain_tree:
job.add_input_file(self.constrain_tree)
job.add_input_file(self.alg_phylip_file)
self.jobs.append(job)
def load_jobs(self):
args = OrderedDict(self.args)
args["-s"] = pjoin(GLOBALS["input_dir"], self.alg_phylip_file)
args["-m"] = self.model_string
args["-n"] = self.alg_phylip_file
if self.constrain_tree:
log.log(24, "Using constrain tree %s" % self.constrain_tree)
args["-g"] = pjoin(GLOBALS["input_dir"], self.constrain_tree)
if self.partitions_file:
log.log(24, "Using alg partitions %s" % self.partitions_file)
args['-q'] = pjoin(GLOBALS["input_dir"], self.partitions_file)
tree_job = Job(self.raxml_bin, args, parent_ids=[self.nodeid])
tree_job.jobname += "-" + self.model_string
tree_job.cores = self.threads
# Register input files necessary to run the job
tree_job.add_input_file(self.alg_phylip_file)
if self.constrain_tree:
tree_job.add_input_file(self.constrain_tree)
if self.partitions_file:
tree_job.add_input_file(self.partitions_file)
self.jobs.append(tree_job)
self.out_tree_file = os.path.join(
tree_job.jobdir, "RAxML_bestTree." + self.alg_phylip_file)
if self.bootstrap == "alrt":
alrt_args = tree_job.args.copy()
if self.constrain_tree:
del alrt_args["-g"]
if self.partitions_file:
alrt_args["-q"] = args['-q']
alrt_args["-f"] = "J"
alrt_args["-t"] = self.out_tree_file
alrt_job = Job(self.raxml_bin,
alrt_args,
parent_ids=[tree_job.jobid])
alrt_job.jobname += "-alrt"
alrt_job.dependencies.add(tree_job)
alrt_job.cores = self.threads
# Register necessary input files
alrt_job.add_input_file(self.alg_phylip_file)
if self.partitions_file:
alrt_job.add_input_file(self.partitions_file)
self.jobs.append(alrt_job)
self.alrt_job = alrt_job
elif self.bootstrap == "alrt_phyml":
alrt_args = {
"-o": "n",
"-i": self.alg_phylip_file,
"--bootstrap": "-2",
"-d": self.seqtype,
"-u": self.out_tree_file,
"--model": self.model,
"--quiet": "",
"--no_memory_check": "",
}
#if self.constrain_tree:
# alrt_args["--constraint_tree"] = self.constrain_tree
alrt_job = Job(self.conf["app"]["phyml"],
alrt_args,
parent_ids=[tree_job.jobid])
alrt_job.add_input_file(self.alg_phylip_file, alrt_job.jobdir)
alrt_job.jobname += "-alrt"
alrt_job.dependencies.add(tree_job)
alrt_job.add_input_file(self.alg_phylip_file)
self.jobs.append(alrt_job)
self.alrt_job = alrt_job
else:
# Bootstrap calculation
boot_args = tree_job.args.copy()
boot_args["-n"] = "bootstraps." + boot_args["-n"]
boot_args["-N"] = int(self.bootstrap)
boot_args["-b"] = 31416
boot_job = Job(self.raxml_bin,
boot_args,
parent_ids=[tree_job.jobid])
boot_job.jobname += "-%d-bootstraps" % (boot_args['-N'])
boot_job.dependencies.add(tree_job)
boot_job.cores = self.threads
# Register necessary input files
boot_job.add_input_file(self.alg_phylip_file)
if self.constrain_tree:
boot_job.add_input_file(self.constrain_tree)
if self.partitions_file:
boot_job.add_input_file(self.partitions_file)
self.jobs.append(boot_job)
# Bootstrap drawing on top of best tree
bootd_args = tree_job.args.copy()
if self.constrain_tree:
del bootd_args["-g"]
if self.partitions_file:
del bootd_args["-q"]
bootd_args["-n"] = "bootstrapped." + tree_job.args["-n"]
bootd_args["-f"] = "b"
bootd_args["-t"] = self.out_tree_file
bootd_args["-z"] = pjoin(boot_job.jobdir,
"RAxML_bootstrap." + boot_job.args["-n"])
bootd_job = Job(self.raxml_bin,
bootd_args,
parent_ids=[tree_job.jobid])
bootd_job.jobname += "-bootstrapped"
bootd_job.dependencies.add(boot_job)
bootd_job.cores = self.threads
self.jobs.append(bootd_job)
self.boot_job = boot_job
self.bootd_job = bootd_job
def load_jobs(self):
args = OrderedDict(self.args)
args["-s"] = pjoin(GLOBALS["input_dir"], self.alg_phylip_file)
args["-m"] = self.model_string
args["-n"] = self.alg_phylip_file
if self.constrain_tree:
log.log(24, "Using constrain tree %s" %self.constrain_tree)
args["-g"] = pjoin(GLOBALS["input_dir"], self.constrain_tree)
if self.partitions_file:
log.log(24, "Using alg partitions %s" %self.partitions_file)
args['-q'] = pjoin(GLOBALS["input_dir"], self.partitions_file)
tree_job = Job(self.raxml_bin, args, parent_ids=[self.nodeid])
tree_job.jobname += "-"+self.model_string
tree_job.cores = self.threads
# Register input files necessary to run the job
tree_job.add_input_file(self.alg_phylip_file)
if self.constrain_tree:
tree_job.add_input_file(self.constrain_tree)
if self.partitions_file:
tree_job.add_input_file(self.partitions_file)
self.jobs.append(tree_job)
self.out_tree_file = os.path.join(tree_job.jobdir,
"RAxML_bestTree." + self.alg_phylip_file)
if self.bootstrap == "alrt":
alrt_args = tree_job.args.copy()
if self.constrain_tree:
del alrt_args["-g"]
if self.partitions_file:
alrt_args["-q"] = args['-q']
alrt_args["-f"] = "J"
alrt_args["-t"] = self.out_tree_file
alrt_job = Job(self.raxml_bin, alrt_args,
parent_ids=[tree_job.jobid])
alrt_job.jobname += "-alrt"
alrt_job.dependencies.add(tree_job)
alrt_job.cores = self.threads
# Register necessary input files
alrt_job.add_input_file(self.alg_phylip_file)
if self.partitions_file:
alrt_job.add_input_file(self.partitions_file)
self.jobs.append(alrt_job)
self.alrt_job = alrt_job
elif self.bootstrap == "alrt_phyml":
alrt_args = {
"-o": "n",
"-i": self.alg_phylip_file,
"--bootstrap": "-2",
"-d": self.seqtype,
"-u": self.out_tree_file,
"--model": self.model,
"--quiet": "",
"--no_memory_check": "",
}
#if self.constrain_tree:
# alrt_args["--constraint_tree"] = self.constrain_tree
alrt_job = Job(self.conf["app"]["phyml"],
alrt_args, parent_ids=[tree_job.jobid])
alrt_job.add_input_file(self.alg_phylip_file, alrt_job.jobdir)
alrt_job.jobname += "-alrt"
alrt_job.dependencies.add(tree_job)
alrt_job.add_input_file(self.alg_phylip_file)
self.jobs.append(alrt_job)
self.alrt_job = alrt_job
else:
# Bootstrap calculation
boot_args = tree_job.args.copy()
boot_args["-n"] = "bootstraps."+boot_args["-n"]
boot_args["-N"] = int(self.bootstrap)
boot_args["-b"] = 31416
boot_job = Job(self.raxml_bin, boot_args,
parent_ids=[tree_job.jobid])
boot_job.jobname += "-%d-bootstraps" %(boot_args['-N'])
boot_job.dependencies.add(tree_job)
boot_job.cores = self.threads
# Register necessary input files
boot_job.add_input_file(self.alg_phylip_file)
if self.constrain_tree:
boot_job.add_input_file(self.constrain_tree)
if self.partitions_file:
boot_job.add_input_file(self.partitions_file)
self.jobs.append(boot_job)
# Bootstrap drawing on top of best tree
bootd_args = tree_job.args.copy()
if self.constrain_tree:
del bootd_args["-g"]
if self.partitions_file:
del bootd_args["-q"]
bootd_args["-n"] = "bootstrapped."+ tree_job.args["-n"]
bootd_args["-f"] = "b"
bootd_args["-t"] = self.out_tree_file
bootd_args["-z"] = pjoin(boot_job.jobdir, "RAxML_bootstrap." + boot_job.args["-n"])
bootd_job = Job(self.raxml_bin, bootd_args,
parent_ids=[tree_job.jobid])
bootd_job.jobname += "-bootstrapped"
bootd_job.dependencies.add(boot_job)
bootd_job.cores = self.threads
self.jobs.append(bootd_job)
self.boot_job = boot_job
self.bootd_job = bootd_job
