示例#1
0
def _ps2pdf(config, out):
    ps_filename = config['combined_ps_name']
    statuslog.info("Converting to PDF")
    cmd = ['ps2pdf', ps_filename, '-']
    capproc.capturedCall(
        cmd, stdout=out, logger=log, check=True)
    statuslog.info("Finished PDF conversion")
def _nprofile(config, out):
    statuslog.info("Calculating n-profile.")
    cmd = [BIN, '-b', ''.join(config["nucleotides"]).upper(),
           config['ddna'], 1, config['length'],
           config['window_size'], config['step'], config['period']]
    capproc.capturedCall(
        cmd, stdout=out, stderr=config['stderr'],
        logger=logger, check=True)
示例#3
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def _extract(config, out):
    gbkfile = config['filename']
    statuslog.debug(
        "Extracting genes in %s.", os.path.basename(gbkfile))
    cmd = [BIN, gbkfile,
           config['GeneDescriptorSkip1'], config['GeneDescriptorKey1'],
           config['GeneDescriptorSkip2'], config['GeneDescriptorKey2']]
    capproc.capturedCall(
        cmd, check=True, logger=logger, stdout=out, stderr=sys.stderr)
示例#4
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def _acgt_gamma(config, dtemp):
    cmd = [BIN, "-q", config["filename"]]
    if "significance" in config:
        cmd.append(str(config["significance"]))

    statuslog.info(
        "Identifying ORFs with 3-base compositional periodicity " "with significance: %s.", config.get("significance")
    )
    log.debug("Starting prediction program in %s", dtemp)
    try:
        capproc.capturedCall(
            cmd, cwd=dtemp, check=True, env={"BASE_DIR_THRESHOLD_TABLES": DATAPATH}, stderr=sys.stderr, logger=log
        )
        log.debug("Prediction finished successfully")
    except capproc.CallProcError as cpe:
        log.error("acgt_gamma exitted with rc: %r", cpe.returncode)
        raise
示例#5
0
def clean_path(path, days):
    "This function actually runs the find and delete."
    logger.info("Cleaning older than: %d @ %r", days, path)
    cmd = ["find", path, "-atime", "+" + str(days), "-delete"]
    return capproc.capturedCall(cmd, logger=logger, stdin=False,
                                stderr_level=logging.WARNING)