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)[source]
Parameters:

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

Return type:

None

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

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)[source]

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)[source]
toil.lib.bioio.setLoggingFromOptions(options)[source]
toil.lib.bioio.getTempFile(suffix='', rootDir=None)[source]