Using GMT from Python by subprocess and shlex packages.

gmt_subprocess.py

# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division,
                        print_function, unicode_literals)
from future_builtins import *
import shlex
import subprocess
import os

script = "gmt --version"
output_file = 'sample.txt'


class ScriptRunningError(Exception):
    pass


def main():
    with open(output_file, 'w') as f:
        proc = subprocess.Popen(shlex.split(script), env=os.environ,
                                stdout=f, stderr=subprocess.PIPE)
    stdout, stderr = proc.communicate()
    retcode = proc.returncode
    del proc

    if retcode == 1:
        raise ScriptRunningError('This script could not run $ %s\n%s' %
                                 (str(script), str(stderr)))
    else:
        return True

if __name__ == '__main__':
    main()

sample.txt

5.1.1