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, 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)