def _run_consensus_jobs(tasks, dry_run=False, cons_json_fn=None):
"""dry_run --- if True, do not actually run the scripts
cons_json_fn --- if not None, write dict{p_id: dict{'script_fn':script_fn, 'script_dir':script_dir}} to it
"""
fns = list()
json_data = dict()
for p_id, (cons_args, fasta_bfn) in tasks.items():
run_dir = "preads"
job_done = "c_%05d_done" % p_id
script_fn = os.path.join(run_dir, "c_%05d.sh" % (p_id))
cons_args["job_done"] = job_done
cons_args["script_fn"] = script_fn
# cons_args <- dict{
# 'out_file_fn': abspath to preads/out.00001.fasta
# 'script_fn' : c_00001.sh
# 'job_done' : c_00001_done
# 'raw_reads' : raw_reads
# 'config' : config}
support.run_consensus(**cons_args)
mkdir(run_dir)
with cd(run_dir):
if dry_run is False:
run_cmd("bash %s" % os.path.basename(script_fn), sys.stdout, sys.stderr, shell=False)
fns.append(os.path.join(run_dir, fasta_bfn))
# add script_dir to args for scattered tasks to work in the correct dir
json_data[p_id] = {
"script_fn": os.path.basename(script_fn), # 'c_00001.sh'
"script_dir": os.path.join(os.getcwd(), run_dir),
} # '/pbi/.../tasks/falcon_ns.tasks.task_falcon0_run_merge_jobs/preads/'
json_fn = "cons_jobs.json" if cons_json_fn is None else cons_json_fn
with open(json_fn, "w") as writer:
writer.write(json.dumps(json_data) + "\n")
return fns # *.fasta ['preads/out.0001.fasta', 'preads/out.00002.fasta', 'preads/out.00003.fasta']
def _run_consensus_jobs(tasks):
fns = list()
for p_id, (cons_args, fasta_bfn) in tasks.items():
run_dir = 'preads'
job_done = "c_%05d_done" %p_id
script_fn = os.path.join(run_dir, "c_%05d.sh" %(p_id))
cons_args['job_done'] = job_done
cons_args['script_fn'] = script_fn
support.run_consensus(**cons_args)
run_cmd('bash %s' %script_fn, sys.stdout, sys.stderr, shell=False)
fns.append(os.path.join(run_dir, fasta_bfn))
return fns # *.fasta
def _run_consensus_jobs(tasks):
fns = list()
for p_id, (cons_args, fasta_bfn) in tasks.items():
run_dir = 'preads'
job_done = "c_%05d_done" % p_id
script_fn = os.path.join(run_dir, "c_%05d.sh" % (p_id))
cons_args['job_done'] = job_done
cons_args['script_fn'] = script_fn
support.run_consensus(**cons_args)
run_cmd('bash %s' % script_fn, sys.stdout, sys.stderr, shell=False)
fns.append(os.path.join(run_dir, fasta_bfn))
return fns # *.fasta
def _run_consensus_jobs(tasks, dry_run=False, cons_json_fn=None):
"""dry_run --- if True, do not actually run the scripts
cons_json_fn --- if not None, write dict{p_id: dict{'script_fn':script_fn, 'script_dir':script_dir}} to it
"""
fns = list()
json_data = dict()
for p_id, (cons_args, fasta_bfn) in tasks.items():
run_dir = 'preads'
job_done = "c_%05d_done" % p_id
script_fn = os.path.join(run_dir, "c_%05d.sh" % (p_id))
cons_args['job_done'] = job_done
cons_args['script_fn'] = script_fn
# cons_args <- dict{
# 'out_file_fn': abspath to preads/out.00001.fasta
# 'script_fn' : c_00001.sh
# 'job_done' : c_00001_done
# 'raw_reads' : raw_reads
# 'config' : config}
support.run_consensus(**cons_args)
mkdir(run_dir)
with cd(run_dir):
if dry_run is False:
run_cmd('bash %s' % os.path.basename(script_fn),
sys.stdout,
sys.stderr,
shell=False)
fns.append(os.path.join(run_dir, fasta_bfn))
# add script_dir to args for scattered tasks to work in the correct dir
json_data[p_id] = {
'script_fn': os.path.basename(script_fn), # 'c_00001.sh'
'script_dir': os.path.join(os.getcwd(), run_dir)
} # '/pbi/.../tasks/falcon_ns.tasks.task_falcon0_run_merge_jobs/preads/'
json_fn = "cons_jobs.json" if cons_json_fn is None else cons_json_fn
with open(json_fn, 'w') as writer:
writer.write(json.dumps(json_data) + "\n")
return fns # *.fasta ['preads/out.0001.fasta', 'preads/out.00002.fasta', 'preads/out.00003.fasta']
