auto_process_ngs.command

Provides a single utility class Command which can be used to build command lines to execute applications.

class auto_process_ngs.command.Command(command, *args)

Class for creating and executing command lines

The Command class is intended to help with building and executing command lines.

For example to create a command line to run the Linux ‘ls’ command:

>>> ls = Command('ls')

To add some arguments:

>>> ls.add_args('-l','-tr')

To see the resulting command line:

>>> str(ls)

To run using the subprocess module do:

>>> ls.run_subprocess()
add_args(*args)

Append arguments to the command

property args

Return the arguments as a list

property command

Return the command

property command_line

Return the full command line as a list

property has_exe

Check if the command executable exists

make_wrapper_script(shell=None, filen=None, fp=None, prologue=None, epilogue=None, quote_spaces=False)

Wrap the command in a script

Returns a string which can be injected into a file and run as a script.

Parameters:

  • shell (str) – optional, if set then will be written to the wrapper script shebang (#!)

  • filen (str) – optional, if set then wrapper script will be written to a file with this path

  • fp (File) – optional, if set then must be a File-like object opened for writing, to which the wrapper script will be written

  • prologue (str) – optional, if set then will be written into the script before the command

  • epilogue (str) – optional, if set then will be written into the script after the command

  • quote_spaces (str) – if True then arguments containing whitespace will be wrapped in quotes

Returns:

the wrapper script contents.

Return type:

String

run_subprocess(log=None, err=None, working_dir=None)

Run the command using subprocess.Popen

This runs the command using the subprocess.popen() function and wais for it to finish.

Parameters:

  • log – optional, name of file to write stdout to (defaults to sys.stdout)

  • err – optional, name of file to write stderr to (defaults to same location as log, if that was specified, or else to sys.stderr)

  • working_dir – optional, working directory to use (defaults to current directory

Returns:

Return code from subprocess.Popen() call.

subprocess_check_output(include_err=True, working_dir=None)

Run the command and capture the output

This runs the command using subprocess.check_output and returns the output (along with the return code from the command).

Parameters:

  • include_err – optional, if True then stderr is included in the output (default); otherwise stderr is discarded.

  • working_dir – optional, working directory to use (defaults to current directory

Returns:

Tuple of (returncode,output).