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)
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)
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
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)