Source code for HTSeqCountCluster.pbsjob.pbsutils

"""Collection of tools for using PBS, a job scheduler for high-performance
computing environments. The command is usually `qsub <options>` on most
systems.
"""
import random
import string
from string import Template


def basejobids(length, name='submit'):
    """"Create base job id and name.

    :param length: [description]
    :type length: [type]
    :param name: [description], defaults to 'submit'
    :type name: str, optional
    :return: [description]
    :rtype: [type]
    """
    base_id = random_id(length=length)
    base = name + "_{0}".format(base_id)

    return base_id, base


def import_temp(filepath):
    """Import a template file that has template strings.

    :param filepath: [description]
    :type filepath: [type]
    """
    file_temp = open(filepath, 'r')
    file_str = file_temp.read()
    file_temp.close()

    file_temp = Template(file_str)
    return file_temp


def file_to_str(filepath):
    """Turn the contents of a file (python file) into a string.

    :param filepath: [description]
    :type filepath: [type]
    """
    file_temp = open(filepath, 'r')
    file_str = file_temp.read()
    return file_str


def random_id(length=5):
    """Generate a random ID of 5 characters to append to qsub job name."""
    return ''.join(random.sample(string.ascii_letters + string.digits, length))


def write_code_file(filename, code, language):
    """Create a python file and write the code to it."""
    if language == 'python':
        with open(filename + '.py', 'w') as pyfile:
            pyfile.write(code)
            pyfile.close()

    elif language == 'bash':
        with open(filename + '.sh', 'w') as bashfile:
            bashfile.write(code)
            bashfile.close()

    elif language == 'R' or 'r':
        with open(filename + '.R', 'w') as rfile:
            rfile.write(code)
            rfile.close()
    else:
        raise NotImplementedError('%s is unsupported.' % language)