toil.lib.bioio

Attributes

logger
root_logger

Functions

set_logging_from_options(options)
get_temp_file([suffix, rootDir])	Return a string representing a temporary file, that must be manually deleted.
system(command)	A convenience wrapper around subprocess.check_call that logs the command before passing it
getLogLevelString([logger])
setLoggingFromOptions(options)
getTempFile([suffix, rootDir])

Module Contents

toil.lib.bioio.logger

toil.lib.bioio.root_logger

toil.lib.bioio.set_logging_from_options(options)

Parameters:

options (Union[toil.common.Config, argparse.Namespace])

Return type:

None

toil.lib.bioio.get_temp_file(suffix='', rootDir=None)

Return a string representing a temporary file, that must be manually deleted.

Parameters:

• suffix (str)

• rootDir (Optional[str])

Return type:

str

toil.lib.bioio.system(command)

A convenience wrapper around subprocess.check_call that logs the command before passing it on. The command can be either a string or a sequence of strings. If it is a string shell=True will be passed to subprocess.check_call. :type command: str | sequence[string]

toil.lib.bioio.getLogLevelString(logger=None)

toil.lib.bioio.setLoggingFromOptions(options)

toil.lib.bioio.getTempFile(suffix='', rootDir=None)