slimutil.py

# Author: Sam Champer

# Functions to run SLiM and to configure command line arguments for SLiM.

import subprocess


def run_slim(command_line_args):
    """
    Runs SLiM using subprocess.
    Args:
        command_line_args: list; a list of command line arguments.
    return: The entire SLiM output as a string.
    """
    slim = subprocess.Popen(command_line_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
    out, err = slim.communicate()
    return out


def configure_slim_command_line(args_dict):
    """
    Sets up a list of command line arguments for running SLiM.
    Args:
        args_dict: a dictionary arguments from arg parser.
    Return
        clargs: A formated list of the arguments.
    """
    clargs = "slim "
    # The filename of the source file must be the last argument:
    source = args_dict.pop("src")
    # Add each argument from arg parser to the command line arguemnts for SLiM:
    for arg in args_dict:
        if isinstance(args_dict[arg], bool):
            clargs += f"-d {arg}={'T' if args_dict[arg] else 'F'} "
        else:
            clargs += f"-d {arg}={args_dict[arg]} "
    # Add the source file, and return the string split into a list.
    clargs += source
    return clargs.split()