SRA sample to unaligned bam using sra tools and sambamba, job submission through slurm

sra2bam.py

from argparse import ArgumentParser
import sys
from pypiper import NGSTk
import textwrap

global tk
tk = NGSTk()

def sra2bam(sra_acession, output_bam):
    # Slurm header
    cmd = tk.slurm_header("_".join(["sra2bam", sra_acession]), "%s_sra2bam.log" % sra_acession, cpus_per_task=4)

    # SRA to BAM
    cmd += "\t\tsam-dump {0} | sambamba view -t 4 -S -f bam /dev/stdin > {0}.bam".format(sra_acession)
    # Slurm footer
    cmd += tk.slurm_footer() + "\n"

    # Write job to file
    job_file = "/scratch/users/arendeiro/%s_sra2bam.sh" % sra_acession
    with open(job_file, "w") as handle:
        handle.write(textwrap.dedent(cmd))

    # Submit
    tk.slurm_submit_job(job_file)

if __name__ == "__main__":
    try:
        parser = ArgumentParser(
            description="Makes unaligned bam file from SRA sample acession number",
            usage="python sra2bam.py <sra_acession> <output_bam>"
        )
        # positional arguments
        parser.add_argument("sra_acession", help="SRA acession number.")
        parser.add_argument("output_bam", help="Output bam file.")
        # parse
        args = parser.parse_args()

        sra2bam(args.sra_acession, args.output_bam)
    except KeyboardInterrupt:
        print("Program canceled by user!")
        sys.exit(1)