Python universal_sys_call示例

示例#1

文件： alignment.py 项目： GiovanniCS/PanDelosFragments

def align_bwa_pe_lib(command,
                     index,
                     reads_file1,
                     reads_file2,
                     work_dir,
                     log,
                     threads=1):
    log.info("Aligning paired-end library")
    log.info("Left reads: " + reads_file1)
    log.info("Right reads: " + reads_file2)
    log.info("Output directory: " + work_dir)
    if os.path.exists(work_dir):
        shutil.rmtree(work_dir)
    os.makedirs(work_dir)
    log_file = os.path.join(work_dir, "output.log")
    err_log_file = os.path.join(work_dir, "err_output")
    result = os.path.join(work_dir, "alignment.sam")
    log.info("Starting alignment of reads using bwa. See detailed log in " +
             log_file)
    log.info("Starting read alignment. See detailed log in " + log_file)
    support.universal_sys_call([
        command, "mem", "-t",
        str(threads), "-S", "-M", index, reads_file1, reads_file2
    ], log, result, err_log_file)
    log.info("Done. See result in " + result)
    return result

示例#2

文件： alignment.py 项目： UNR-CFB/bch-709-intro-bioinformatics-2015f

def align_bwa_pe_lib(command,
                     index,
                     reads_file1,
                     reads_file2,
                     work_dir,
                     log,
                     threads=1):
    log.info("Aligning paired-end library")
    log.info("Left reads: " + reads_file1)
    log.info("Right reads: " + reads_file2)
    log.info("Output directory: " + work_dir)
    if os.path.exists(work_dir):
        shutil.rmtree(work_dir)
    os.makedirs(work_dir)
    log_file = os.path.join(work_dir, "output.log")
    err_log_file = os.path.join(work_dir, "err_output")
    result = os.path.join(work_dir, "alignment.sam")
    log.info("Starting alignment of reads using bwa. See detailed log in " +
             log_file)
    log.info("Starting read alignment. See detailed log in " + log_file)
    support.universal_sys_call([
        command, "mem", index, reads_file1, reads_file2, "-t",
        str(threads), "-S", "-M"
    ], log, result, err_log_file)
    log.info("Done. See result in " + result)
    return result

示例#3

文件： alignment.py 项目： B-UMMI/INNUca

def index_bwa(command, log, reference, work_dir, algorithm = "is"):
    if os.path.exists(work_dir):
        shutil.rmtree(work_dir)
    os.makedirs(work_dir)
    log.info("Constructing bwa index")
    index = os.path.join(work_dir, "index")
    log_file = os.path.join(work_dir, "output.log")
    err_log_file = os.path.join(work_dir, "err_output")
    log.info(" ".join([command, "index", "-a", algorithm, "-p", index, reference]))
    support.universal_sys_call([command, "index", "-a", algorithm, "-p", index, reference], log, log_file, err_log_file)
    log.info("Index constructed.")
    return index

示例#4

文件： alignment.py 项目： GiovanniCS/PanDelosFragments

def index_bwa(command, log, reference, work_dir, algorithm="is"):
    if os.path.exists(work_dir):
        shutil.rmtree(work_dir)
    os.makedirs(work_dir)
    log.info("Constructing bwa index")
    index = os.path.join(work_dir, "index")
    log_file = os.path.join(work_dir, "output.log")
    err_log_file = os.path.join(work_dir, "err_output")
    log.info(" ".join(
        [command, "index", "-a", algorithm, "-p", index, reference]))
    support.universal_sys_call(
        [command, "index", "-a", algorithm, "-p", index, reference], log,
        log_file, err_log_file)
    log.info("Index constructed.")
    return index