def __init__(self, job_name, out_sh=None, queue_type='PBS',
directory='./', submit=True):
cmd_list = []
for file in glob('{}/*sam'.format(directory)):
cmd_list.append(
'samtools view -bS -q 10 {} > {}.bam'.format(file, file))
sub = Submitter(queue_type=queue_type,
sh_filename=out_sh,
commands=cmd_list,
job_name=job_name, nodes=1, ppn=1, queue='home',
walltime='1:00:00',
array=True, max_running=20)
sub.job(submit=submit)
def __init__(self, job_name, out_sh=None,
directory='./', submit=True):
command_list = []
for file in glob('{}/*sorted.bam'.format(directory)):
command_list.append('samtools index {0}'.format(file))
# def submit_and_write(name, command_list):
sub = Submitter(queue_type='PBS', sh_filename=out_sh,
commands=command_list,
job_name=job_name, nodes=1, ppn=1, queue='home',
array=True,
max_running=20, walltime='0:30:00')
sub.job(submit=submit)
def __init__(self, job_name, out_sh=None,
directory='./', submit=True):
cmd_list = []
for file in glob('{}/*bam'.format(directory.rstrip('/'))):
cmd_list.append(
"samtools view -h -F 4 {0} | awk '$6 !~ /N/ || $1 ~ /@/' "
"| "
"samtools view -bS - > {0}.unspliced.bam".format(file))
sub = Submitter(queue_type='PBS', sh_filename=out_sh,
commands=cmd_list,
job_name=job_name, nodes=1, ppn=16, queue='home',
array=True,
walltime='0:30:00',
max_running=10)
sub.job(submit=submit)
def __init__(self, job_name, out_sh=None, directory='./', submit=True):
cmd_list = []
for file in glob('{}/*bam'.format(directory.rstrip('/'))):
cmd_list.append(
"samtools view -h -F 4 {0} | awk '$6 !~ /N/ || $1 ~ /@/' "
"| "
"samtools view -bS - > {0}.unspliced.bam".format(file))
sub = Submitter(queue_type='PBS',
sh_filename=out_sh,
commands=cmd_list,
job_name=job_name,
nodes=1,
ppn=16,
queue='home',
array=True,
walltime='0:30:00',
max_running=10)
sub.job(submit=submit)
def __init__(self, job_name, out_sh=None, directory='./', submit=True):
command_list = []
for file in glob('{}/*sorted.bam'.format(directory)):
command_list.append('samtools index {0}'.format(file))
# def submit_and_write(name, command_list):
sub = Submitter(queue_type='PBS',
sh_filename=out_sh,
commands=command_list,
job_name=job_name,
nodes=1,
ppn=1,
queue='home',
array=True,
max_running=20,
walltime='0:30:00')
sub.job(submit=submit)
def __init__(self,
job_name,
out_sh=None,
queue_type='PBS',
directory='./',
submit=True):
cmd_list = []
for file in glob('{}/*sam'.format(directory)):
cmd_list.append('samtools view -bS -q 10 {} > {}.bam'.format(
file, file))
sub = Submitter(queue_type=queue_type,
sh_filename=out_sh,
commands=cmd_list,
job_name=job_name,
nodes=1,
ppn=1,
queue='home',
walltime='1:00:00',
array=True,
max_running=20)
sub.job(submit=submit)
