#!/usr/bin/env python3

__author__ = "Darrin Lemmer"
__version__ = "1.0.0"
__email__ = "dlemmer@tgen.org"

'''
Created on Jun 11, 2014

@author: dlemmer
'''

from nasp import __version__ as nasp_version
import logging
import os
import re


try:
    import readline
    import glob

    def complete(text, state):
        """
        Tab autocomplete for prompts.

        Args:
            text (str): current user input
            state (int): index from 0 to n until the function returns a non-string value

        Returns:
            str: matching file at the current state index
        """
        matches = glob.glob(text+'*')
        return matches[state] + os.sep if os.path.isdir(matches[state]) else matches[state]

    readline.set_completer_delims('')
    readline.parse_and_bind("tab: complete")
    readline.set_completer(complete)
except ImportError:
    # The readline module is unavailable, tab-autocomplete will not work
    pass


def _parse_args():
    import argparse

    parser = argparse.ArgumentParser(prog="nasp",
                                     description="This is the \"Northern Arizona SNP Pipeline\", version %s" % nasp_version)
    parser.add_argument("reference_fasta", nargs="?", default="", help="Path to the reference fasta.")
    parser.add_argument("output_folder", nargs="?", default="", help="Folder to store the output files.")
    parser.add_argument("--config", help="Path to the configuration xml file.")
    return parser.parse_args()


def _expand_path(path):
    user_match = re.match('^(~)(.*)$', path)
    if user_match:
        path = os.path.expanduser(path)
    return os.path.abspath(path)


def _create_file_tuple(path):
    name = os.path.splitext(os.path.basename(path))[0]
    return name, path


def _find_files(path, extension):
    file_list = []
    for file in os.listdir(path):
        is_type = re.search('(.*)(\.%s)$' % extension, file, re.IGNORECASE)
        if is_type:
            sample_name = is_type.group(1)
            file_list.append((sample_name, os.path.join(path, file)))
            logging.info((sample_name, os.path.join(path, file)))
    return file_list


def _find_executable(application):  # This method is not OS-independent. Should work on a better way
    import subprocess

    executable = ""
    try:
        executable = subprocess.check_output(["which", application])
    except subprocess.CalledProcessError:
        try:
            executable = subprocess.check_output("find ~ -name %s" % application, shell=True)
        except subprocess.CalledProcessError as cpe:
            executable = cpe.output
    match = re.search('^(.*)\n.*$', str(executable, "utf-8"))
    if match:
        executable = match.group(1)
    return executable


def _find_reads(path):
    read_list = []
    for file in os.listdir(path):
        is_read = re.search('(.*)(\.fastq(?:\.gz)?)$', file, re.IGNORECASE)
        if is_read:
            sample_name = is_read.group(1)
            is_paired = re.search('^(.*)(_[R]?)([12])(.*)$', sample_name, re.IGNORECASE)
            if is_paired:
                if is_paired.group(3) == '1':  # If paired, only process read 1, so we don't double count the pair
                    sample_name = is_paired.group(1)
                    read1 = file
                    read2 = "%s%s2%s%s" % (is_paired.group(1), is_paired.group(2), is_paired.group(4), is_read.group(2))
                    if os.path.exists(os.path.join(path, read2)):
                        read = (sample_name, os.path.join(path, read1), os.path.join(path, read2))
                        read_list.append(read)
                        logging.info(read)
                    else:
                        logging.warning("Cannot find %s, the matching read to %s. Skipping..." % (read2, read1))
            else:
                read = (sample_name, os.path.join(path, file))
                read_list.append(read)
                logging.info(read)
    return read_list


def _get_bams(cwd):
    bam_list = []
    response = input("\nDo you have pre-aligned SAM/BAM files you wish to include [N]? ")
    if re.match('^[Yy]', response):
        path = input("Where are these files located [%s]? " % cwd)
        path = _expand_path(path) if path else cwd
        logging.info("Looking for sams/bams in %s...", path)
        bam_list = _find_files(path, "bam")
        bam_list.extend(_find_files(path, "sam"))
    return bam_list


def _get_vcfs(cwd):
    vcf_list = []
    response = input("\nDo you have pre-called VCFfiles you wish to include [N]? ")
    if re.match('^[Yy]', response):
        path = input("Where are these files located [%s]? " % cwd)
        path = _expand_path(path) if path else cwd
        logging.info("Looking for vcfs in %s...", path)
        vcf_list = _find_files(path, "vcf")
    return vcf_list


def _get_external_fastas(cwd, exclude):
    fasta_list = []
    response = input("\nDo you have fasta files for external genomes you wish to include [Y]? ")
    if not re.match('^[Nn]', response):
        path = input("Where are these files located [%s]? " % cwd)
        path = _expand_path(path) if path else cwd
        logging.info("Looking for external fastas in %s...", path)
        fasta_list = _find_files(path, "(?:fa|fna|fas|fasta)$")
        # remove the reference from the fasta_list if it is in there
        for fasta_tuple in fasta_list:
            fasta = fasta_tuple[1]
            if fasta == exclude:
                fasta_list.remove(fasta_tuple)
    return fasta_list


def _get_reads(cwd):
    read_list = []
    response = input("\nDo you have read files you wish to include [Y]? ")
    if not re.match('^[Nn]', response):
        path = input("Where are these files located [%s]? " % cwd)
        path = _expand_path(path) if path else cwd
        logging.info("Looking for read files in %s...", path)
        read_list = _find_reads(path)
    return read_list


def _get_application_path(application):
    app_path = _find_executable(application)
    if not app_path:
        app_path = input("\nUnable to find '%s', please enter the full path to '%s': " % (application, application))
    while not os.access(app_path, os.X_OK):
        app_path = input(
            "\n'%s' either does not exist or you don't have permission to run it, please enter the full path to '%s': " % (
            app_path, application))
    return app_path


# TODO(jtravis): search CLASSPATH
# NOTE: Wildcard characters are allowed in 'jarfile' as both fnmatch and glob will handle them
def _get_java_path(jarfile):
    import fnmatch
    paths = ['/usr/share/java/']
    paths.extend(os.environ['PATH'].split(os.pathsep))
    for path in paths:
        match_list = glob.glob(os.path.join(path, jarfile))
        if match_list:
            return match_list[0]
    # Didn't find it in path, check user's home directory
    for path, dirs, files in os.walk(os.path.expanduser("~")):
        for filename in fnmatch.filter(files, jarfile):
            return os.path.join(path, filename)
    #Didn't find it there, recursively check current directory
    for path, dirs, files in os.walk(os.getcwd()):
        for filename in fnmatch.filter(files, jarfile):
            return os.path.join(path, filename)
    #Let's ask the user
    jar_path = input("\nUnable to find '%s', please enter the full path to '%s': " % (jarfile, jarfile))
    while not os.access(jar_path, os.R_OK) or not os.path.isfile(jar_path):
        # If the user entered a directory path instead of a complete path, check if the file exists in the directory
        if os.path.isdir(jar_path):
            for path in os.listdir(jar_path):
                if path.endswith(os.pathsep + jarfile):
                    return path
        jar_path = input(
            "\n'%s' either does not exist or you don't have permission to run it, please enter the full path to '%s': " % (
            jar_path, jarfile))
    return jar_path


def _get_advanced_settings(app_name, app_path, app_args, job_parms):
    response = input("Would you like to set advanced %s settings [N]? " % app_name)
    if re.match('^[Yy]', response):
        alt_version = input("  Would you like to use an alternate %s version [N]? " % app_name)
        if re.match('^[Yy]', alt_version):
            path = input("    What is the full path to the %s runtime you wish to use [%s]? " % (app_name, app_path))
            path = path if path else app_path
            while not os.access(path, os.X_OK):
                path = input(
                    "    '%s' either does not exist or you don't have permission to run it, please enter the full path to '%s': " % (
                    path, app_name))
            app_path = path
        args = input("  What additional arguments would you like to pass to %s [%s]? " % (app_name, app_args))
        if args:
            app_args = args
        queue = input("  What queue/partition should %s run on [%s]? " % (app_name, job_parms['queue']))
        if queue:
            job_parms['queue'] = queue
        mem = input("  How much memory (GB) will %s require [%s]? " % (app_name, job_parms['mem_requested']))
        if re.match("^[1-9][0-9]*$", mem):
            job_parms['mem_requested'] = mem
        cpus = input("  How many CPUs do you want %s to use [%s]? " % (app_name, job_parms['num_cpus']))
        if re.match("^[1-9][0-9]*$", cpus):
            job_parms['num_cpus'] = cpus
        hours = input("  How many hours will %s take to run [%s]? " % (app_name, job_parms['walltime']))
        if re.match("^[1-9][0-9]*$", hours):
            job_parms['walltime'] = hours
    return app_name, app_path, app_args, job_parms


def _get_aligners(queue, args):
    aligner_list = []
    bwa_path = ""
    print(
        "\nThis pipeline currently supports four aligners: BWA, Bowtie2, Novoalign, and SNAP.\nYou can also provide pre-aligned BAM files, and you can choose as many options as you want.")
#     response = input("\nWould you like to run BWA samp/se [N]?* ")
#     if re.match('^[Yy]', response):
#         bwa_path = _get_application_path("bwa")
#         bwa_sampe_settings = _get_advanced_settings("BWA-sampe", bwa_path, "",
#                                                     {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36',
#                                                      'queue': queue, 'args': args})
#         aligner_list.append(bwa_sampe_settings)
#         logging.info(bwa_sampe_settings)
    response = input("\nWould you like to run BWA mem [Y]? ")
    if not re.match('^[Nn]', response):
        if not bwa_path:
            bwa_path = _get_application_path("bwa")
        bwa_mem_settings = _get_advanced_settings("BWA-mem", bwa_path, "",
                                                  {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36',
                                                   'queue': queue, 'args': args})
        aligner_list.append(bwa_mem_settings)
        logging.info(bwa_mem_settings)
    response = input("\nWould you like to run Bowtie2 [Y]? ")
    if not re.match('^[Nn]', response):
        bt2_path = _get_application_path("bowtie2")
        bt2_settings = _get_advanced_settings("Bowtie2", bt2_path, "",
                                              {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36', 'queue': queue,
                                               'args': args})
        aligner_list.append(bt2_settings)
        logging.info(bt2_settings)
    response = input("\nWould you like to run Novoalign [N]? ")
    if re.match('^[Yy]', response):
        novo_path = _get_application_path("novoalign")
        novo_settings = _get_advanced_settings("Novoalign", novo_path, "-r all",
                                               {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36',
                                                'queue': queue, 'args': args})
        aligner_list.append(novo_settings)
        logging.info(novo_settings)
    response = input("\nWould you like to run SNAP [N]? ")
    if re.match('^[Yy]', response):
        snap_path = _get_application_path("snap_aligner")
        #Add -M option by default to make SNAP generate traditional CIGAR strings in the BAM output to be more compatible with SNP callers
        snap_settings = _get_advanced_settings("SNAP", snap_path, "-M",
                                               {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36',
                                                'queue': queue, 'args': args})
        aligner_list.append(snap_settings)
        logging.info(snap_settings)
    return aligner_list


def _get_snpcallers(queue, args):
    snpcaller_list = []
    using_gatk = False
    print(
        "\nThis pipeline currently supports four SNP callers: GATK, SolSNP, VarScan, and SAMtools, and you can provide VCF files.\nYou can choose as many options as you want.")
    response = input("\nWould you like to run GATK [Y]? ")
    if not re.match('^[Nn]', response):
        gatk_path = _get_java_path("GenomeAnalysisTK.jar")
        gatk_settings = _get_advanced_settings("GATK", gatk_path, "-stand_call_conf 100 -stand_emit_conf 100 -ploidy 1",
                                               {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36',
                                                'queue': queue, 'args': args})
        snpcaller_list.append(gatk_settings)
        logging.info(gatk_settings)
        using_gatk = True
    response = input("\nWould you like to run SolSNP [N]? ")
    if re.match('^[Yy]', response):
        solsnp_path = _get_java_path("SolSNP.jar")
        solsnp_settings = _get_advanced_settings("SolSNP", solsnp_path, "",
                                                 {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36',
                                                  'queue': queue, 'args': args})
        snpcaller_list.append(solsnp_settings)
        logging.info(solsnp_settings)
    response = input("\nWould you like to run VarScan [Y]? ")
    if not re.match('^[Nn]', response):
        varscan_path = _get_java_path("VarScan.jar")
        varscan_settings = _get_advanced_settings("VarScan", varscan_path, "",
                                                  {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36',
                                                   'queue': queue, 'args': args})
        snpcaller_list.append(varscan_settings)
        logging.info(varscan_settings)
    response = input("\nWould you like to run SAMtools [Y]? ")
    if not re.match('^[Nn]', response):
        samtools_path = _get_application_path("bcftools")
        samtools_settings = _get_advanced_settings("SAMtools", samtools_path, "",
                                                   {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36',
                                                    'queue': queue, 'args': args})
        snpcaller_list.append(samtools_settings)
        logging.info(samtools_settings)
    return snpcaller_list, using_gatk


def _get_job_submitter():
    job_submitter = "invalid"
    queue = ""
    args = ""
    response = input(
        "\nWhat system do you use for job management (PBS/TORQUE, SLURM, SGE/OGE, and 'none' are currently supported) [PBS]? ")
    while job_submitter == "invalid":
        if re.match('^(PBS|Torque|qsub)$', response, re.IGNORECASE) or response == "":
            job_submitter = "PBS"
        elif re.match('^(SLURM|sbatch)$', response, re.IGNORECASE):
            job_submitter = "SLURM"
        elif re.match('^(SGE|OGE)', response, re.IGNORECASE):
            job_submitter = "SGE"
        elif re.match('^none$', response, re.IGNORECASE):
            job_submitter = "NONE"
        else:
            response = input("  %s is not a valid job management system, please enter another [PBS]? " % response)
    if job_submitter != "NONE":
        queue = input(
            "  Would you like to specify a queue/partition to use for all jobs (leave blank to use default queue) []? ")
        args = input("  What additional arguments do you need to pass to the job management system []? ")
    return job_submitter, queue, args


def _get_trimming_parameters(queue, args):
    import pkg_resources
    trim_path = _get_java_path("trimmomatic*.jar")
    adapter_file = pkg_resources.resource_filename('nasp', 'illumina_adapters_all.fasta')
    quality_string = ''
    response = input("  What adapter file are you using for trimming [%s]? " % adapter_file)
    if response:
        adapter_file = response
    response = input("  Would you also like to perform quality trimming [N]? ")
    if re.match('^[Yy]', response):
        quality_string = 'SLIDINGWINDOW:5:20'
        response = input("  What quality trimming parameters do you want to use [%s]? " % quality_string)
        if response:
            quality_string = response
    min_length = "80"
    response = input("  What is the minimum length read to keep after trimming [%s]? " % min_length)
    if response:
        min_length = response
    arg_string = "ILLUMINACLIP:%s:2:30:10 %s MINLEN:%s" % (adapter_file, quality_string, min_length)
    return _get_advanced_settings("ReadTrimmer", trim_path, arg_string,
                                  {'num_cpus': '4', 'mem_requested': '6', 'walltime': '24', 'queue': queue, 'args': args})


def _get_user_input(reference, output_folder):
    import sys

    configuration = {}
    cwd = os.getcwd()

    print("Welcome to NASP version %s." % nasp_version)

    if not output_folder:
        output_folder = input("\nWhere would you like output files to be written [nasp_results]? ")
        if not output_folder:
            output_folder = "nasp_results"
    output_folder = _expand_path(output_folder)
    if os.path.exists(output_folder):
        response = input(
            "\nOutput folder %s already exists!\nFiles in it may be overwritten!\nShould we continue anyway [N]? " % output_folder)
        if not re.match('^[Yy]', response):
            print("Operation cancelled!")
            quit()
    else:
        os.makedirs(output_folder)
    configuration["output_folder"] = output_folder

    logfile = os.path.join(output_folder, "runlog.txt")
    logging.basicConfig(level=logging.DEBUG,
                        format='%(asctime)s %(levelname)-8s %(message)s',
                        datefmt='%m/%d/%Y %H:%M:%S',
                        filename=logfile,
                        filemode='w')

    logging.info("$PATH="+os.environ.get("PATH", ""))
    logging.info("$PYTHONPATH="+os.environ.get("PYTHONPATH", ""))
    if "LOADEDMODULES" in os.environ:
        logging.info("LOADEDMODULES="+os.environ.get("LOADEDMODULES", ""))

    if not reference:
        reference = input("\nWhere is the reference fasta file you would like to use? ")
        while not os.access(reference, os.R_OK) or not os.path.isfile(reference):
            reference = input("\n'%s' either does not exist or you don't have permission to access it, please enter the path to the reference fasta file you would like to use: " % reference)
    reference = _expand_path(reference)
    configuration["reference"] = _create_file_tuple(reference)
    logging.info("Reference = %s", configuration["reference"])

    response = input(
        "\nDo you want to check the reference for duplicated regions\nand skip SNPs that fall in those regions [Y]? ")
    configuration["find_dups"] = "False" if re.match('^[Nn]', response) else "True"
    logging.info("FindDups = %s", configuration["find_dups"])

    (job_submitter, queue, args) = _get_job_submitter()
    configuration["job_submitter"] = job_submitter
    logging.info("JobSubmitter = %s", configuration["job_submitter"])

    name_match = re.search('^.*/(.*)$',
                           output_folder)  # Warning, not OS-independent! Should find a better way to do this.
    configuration["run_name"] = name_match.group(
        1)  # Temporary: setting the run name to be whatever the the output folder is named. Should ask user.
    logging.info("RunName = %s", configuration["run_name"])

    samtools_path = _find_executable("samtools")
    configuration["samtools"] = ("Samtools", samtools_path, "", {})
    logging.info("Samtools = %s", configuration["samtools"])

    run_path = os.path.abspath(os.path.dirname(sys.argv[0]))
    configuration["index"] = ("Index", run_path, "",
                              {'name': 'nasp_index', 'num_cpus': '1', 'mem_requested': '2', 'walltime': '4',
                               'queue': queue, 'args': args})
    logging.info("Index = %s", configuration["index"])

    fasta_list = _get_external_fastas(cwd, reference)
    configuration["assemblies"] = fasta_list

    if configuration["find_dups"] or len(fasta_list) > 0:
        nucmer_path = _get_application_path("nucmer")
        nucmer_args = ""
        if len(fasta_list) > 0:
            deltafilter_path = _get_application_path("delta-filter")
            deltafilter_args = ""
            response = input("  Would you like to set advanced NUCmer settings [N]? ")
            if re.match('^[Yy]', response):
                nucmer_args = input(
                    "  What additional arguments would you like to pass to 'nucmer' while importing external genomes? ")
                deltafilter_args = input(
                    "  What additional arguments would you like to pass to 'delta-filter' while importing external genomes? ")
            configuration["assembly_importer"] = ("AssemblyImporter", deltafilter_path, deltafilter_args,
                                                  {'num_cpus': '1', 'mem_requested': '4', 'walltime': '4',
                                                   'queue': queue, 'args': args})
            logging.info("AssemblyImporter = %s", configuration["assembly_importer"])
        configuration["dup_finder"] = ("DupFinder", nucmer_path, nucmer_args,
                                       {'num_cpus': '1', 'mem_requested': '4', 'walltime': '4', 'queue': queue,
                                        'args': args})
        logging.info("DupFinder = %s", configuration["dup_finder"])

    read_list = _get_reads(cwd)
    configuration["reads"] = read_list

    if len(read_list) > 0:
        response = input("\nWould you like to use Trimmomatic to trim your reads first [N]? ")
        if re.match('^[Yy]', response):
            configuration["trim_reads"] = "True"
            configuration["read_trimmer"] = _get_trimming_parameters(queue, args)
            logging.info("ReadTrimmer = %s", configuration["read_trimmer"])
        logging.info("Getting Aligners...")
        configuration["aligners"] = _get_aligners(queue, args)
    else:
        configuration["aligners"] = []

    bam_list = _get_bams(cwd)
    configuration["alignments"] = bam_list
    if len(bam_list) > 0:
        configuration["bam_index"] = ("BamIndex", run_path, "",
                                      {'name': 'nasp_bamindex', 'num_cpus': '1', 'mem_requested': '2', 'walltime': '4',
                                       'queue': queue, 'args': args})
        logging.info("BamIndex = %s", configuration["bam_index"])

    if len(read_list) > 0 or len(bam_list) > 0:
        logging.info("Getting SNP Callers...")
        (configuration["snpcallers"], using_gatk) = _get_snpcallers(queue, args)

        if using_gatk:
            picard_path = _get_java_path("picard.jar")
            configuration["picard"] = ("Picard", picard_path, "", {})
            logging.info("Picard = %s", configuration["picard"])
    else:
        configuration["snpcallers"] = []

    vcf_list = _get_vcfs(cwd)
    configuration["vcfs"] = vcf_list

    if len(read_list) > 0 or len(bam_list) > 0 or len(vcf_list) > 0:
        coverage_filter = input(
            "\nThis pipeline can do filtering based on coverage.\nIf you do not want filtering based on coverage, enter 0.\nWhat is your minimum coverage threshold [10]? ")
        if not coverage_filter:
            coverage_filter = 10
        configuration["coverage_filter"] = str(coverage_filter)
        logging.info("CoverageFilter = %s", configuration["coverage_filter"])

        proportion_filter = input(
            "\nThis pipeline can do filtering based on the proportion of reads that match the call made by the SNP caller.\nIf you do not want filtering based on proportion, enter 0.\nWhat is the minimum acceptable proportion [0.9]? ")
        if not proportion_filter:
            proportion_filter = 0.9
        configuration["proportion_filter"] = str(proportion_filter)
        logging.info("ProportionFilter = %s", configuration["proportion_filter"])

    matrix_settings = _get_advanced_settings("MatrixGenerator", gonasp_path(), "", {'name':'nasp_matrix', 'num_cpus':'8', 'mem_requested':'8', 'walltime':'48', 'queue':queue, 'args':args})
    configuration["matrix_generator"] = matrix_settings
    logging.info("MatrixGenerator = %s", configuration["matrix_generator"])

    include_allref_pos = input("\nDo you want to create a master_masked matrix that includes all positions with low-quality positions that failed the coverage or proportion filter masked with an 'N' [N]? ")
    if re.match('^[Yy]', include_allref_pos):
        configuration["filter_matrix_format"] = "include_allref_pos"
        logging.info("FilterMatrixFormat = %s", configuration["filter_matrix_format"])

    return configuration


def gonasp_path():
    import sys
    import pkg_resources
    if sys.maxsize > 2**32:
        matrix_path = pkg_resources.resource_filename('nasp', 'nasptool_linux_64')
    else:
        matrix_path = pkg_resources.resource_filename('nasp', 'nasptool_linux_32')
    if os.path.exists(matrix_path):
        return matrix_path
    else:
        return "nasptool_linux_64"


# def guess_job_manager():
#     try:
#         import os
#         import shutil
#         # Order matters.
#         # SLURM includes a simple qsub wrapper
#         # TORQUE and SGE/OGE use variations of qsub
#         if shutil.which('sbatch'):
#             return 'SLURM'
#         elif os.environ.get('SGE_ROOT') is not None:
#             return 'SGE'
#         elif shutil.which('qsub'):
#             return 'PBS'
#         else:
#             return 'NONE'
#     except ImportError:
#         return 'NONE'


def main():
    import sys
    import nasp.dispatcher as dispatcher
    import nasp.configuration_parser as configuration_parser

    # This is hack to forward commands to gonasp
    if len(sys.argv) > 1 and sys.argv[1] in ['help', 'duplicates', 'frankenfasta', 'matrix', 'export']:
        if sys.argv[1] == 'help' or any(arg in ['-h', '-help', '--help'] for arg in sys.argv) or len(sys.argv) < 3:
            print("Requesting nasp internal command usage message. Enter 'nasp --help' for the nasp pipeline usage message.")
            print("Unlike the nasp pipeline, these commands will not be automatically submitted to your job manager")
        import subprocess
        subprocess.call([gonasp_path()] + sys.argv[1:])
        return

    commandline_args = _parse_args()
    if commandline_args.config:
        configuration = configuration_parser.parse_config(commandline_args.config)
        output_folder = configuration["output_folder"]
        if os.path.exists(output_folder):
            response = input(
                "\nOutput folder %s already exists!\nFiles in it may be overwritten!\nShould we continue anyway [N]? " % output_folder)
            if not re.match('^[Yy]', response):
                print("Operation cancelled!")
                quit()
        else:
            os.makedirs(output_folder)
        logfile = os.path.join(output_folder, "runlog.txt")
        logging.basicConfig(level=logging.DEBUG,
                            format='%(asctime)s %(levelname)-8s %(message)s',
                            datefmt='%m/%d/%Y %H:%M:%S',
                            filename=logfile,
                            filemode='w')
    else:
        configuration = _get_user_input(commandline_args.reference_fasta, commandline_args.output_folder)
    configuration_parser.write_config(configuration)
    dispatcher.begin(configuration)


if __name__ == "__main__":
    main()
