51894da4d9c4c4186c1b4ce34b2cf53737f0dab5,rnaseq/src/run_SamToFastq.py,,,#,10

Before Change

subprocess.check_call("mkfifo /tmp/read1_pipe /tmp/read2_pipe /tmp/read0_pipe", shell=True)

// Set gzip streams
subprocess.check_call("gzip -"+args.gzip+" -c < /tmp/read1_pipe > "+fastq1+" &", shell=True)
subprocess.check_call("gzip -"+args.gzip+" -c < /tmp/read2_pipe > "+fastq2+" &", shell=True)
subprocess.check_call("gzip -"+args.gzip+" -c < /tmp/read0_pipe > "+fastq0+" &", shell=True)

// SamToFastq (write to pipes)
subprocess.check_call("java -jar -Xmx8g /picard-tools/picard.jar SamToFastq INPUT="+args.bam_file\

After Change

    os.makedirs(args.output_dir)

// Make named pipes for gzip
with cd(args.output_dir):
    fastq1 = args.prefix+"_1.fastq.gz"
    fastq2 = args.prefix+"_2.fastq.gz"
    fastq0 = args.prefix+"_unpaired.fastq.gz"

    subprocess.check_call("mkfifo read1_pipe read2_pipe read0_pipe", shell=True)

    // Set gzip streams
    subprocess.check_call("gzip -"+args.gzip+" -c < read1_pipe > "+fastq1+" &", shell=True)
    subprocess.check_call("gzip -"+args.gzip+" -c < read2_pipe > "+fastq2+" &", shell=True)
    subprocess.check_call("gzip -"+args.gzip+" -c < read0_pipe > "+fastq0+" &", shell=True)

    // SamToFastq (write to pipes)
    subprocess.check_call("java -jar -Xmx8g /opt/picard-tools/picard.jar SamToFastq INPUT="+args.bam_file\
        +" INCLUDE_NON_PF_READS="+args.include_non_pf_reads\
        +" INCLUDE_NON_PRIMARY_ALIGNMENTS="+args.include_non_primary_alignments\
        +" VALIDATION_STRINGENCY=SILENT FASTQ=read1_pipe SECOND_END_FASTQ=read2_pipe UNPAIRED_FASTQ=read0_pipe", shell=True)

    // Delete named pipes
    subprocess.check_call("rm read1_pipe read2_pipe read0_pipe", shell=True)

    // Delete unpaired reads FASTQ if empty
    with open(fastq0, "rb") as f0:
        f0.seek(-4,2)
        if struct.unpack("<I", f0.read(4))[0]==0:  // empty file
            os.remove(fastq0)

print("["+datetime.now().strftime("%b %d %H:%M:%S")+"] Finished SamToFastq", flush=True)

Instances