from optparse import OptionParser
from threading import Lock
from os import sep, makedirs
from sys import stderr

LENGTH_ERR = 0.2
MIN_IDENTITY = 0.45
MAX_EVALUE = 1e-30
MIN_ORFLEN = 300
NUM_THREADS = 16
NUM_PROCESSES = 2
DIRECTORY = '.' + sep
PLOTTER = 'biotools.analysis.plot'

START_CODONS = ["ATG"]
STOP_CODONS = ["TAG", "TAA", "TGA"]
args = tuple()

predicting = True
clustering = True
renaming = True
calculating = True
reporting = True
plotting = True
verbose = False

lock = Lock()

parser = OptionParser(usage="Usage: %prog [options] " +
                      "<database> <sequences ...>")
parser.add_option("-S", "--start", action="append", dest="start",
                  default=START_CODONS, type="string",
                  help="define a start codon [default: %s]" %
                  ' '.join("-S " + s for s in START_CODONS))
parser.add_option("-E", "--stop", action="append", dest="stop",
                  default=STOP_CODONS, type="string",
                  help="define a stop codon [default: %s]" %
                  ' '.join("-E " + s for s in STOP_CODONS))
parser.add_option("-j", "--threads", action="store", dest="threads",
                  default=NUM_THREADS, type="int",
                  help="number of threads [default: %default]")
parser.add_option("-p", "--processes", action="store", dest="processes",
                  default=NUM_PROCESSES, type="int",
                  help="number of parallel processes to run " +
                  "[default: %default]")
parser.add_option("-e", "--evalue", action="store", dest="evalue",
                  default=MAX_EVALUE, type="float",
                  help="maximum e-value [default: %default]")
parser.add_option("-I", "--identity", action="store", dest="identity",
                  default=MIN_IDENTITY, type="float",
                  help="minimum percent identity [default: %default]")
parser.add_option("-L", "--length", action="store", dest="fraction",
                  default=LENGTH_ERR, type="float",
                  help="allowable relative error in hit length " +
                  "[default: %default]")
parser.add_option("-O", "--orflen", action="store", dest="orflen",
                  metavar="bases", default=MIN_ORFLEN, type="int",
                  help="minimum allowable length for ORFs [default: %default]")
parser.add_option("-d", "--directory", action="store", dest="directory",
                  default=DIRECTORY, type="string",
                  help="set working directory [default: current]")
parser.add_option("-P", "--plotter", action="store", dest="plotter",
                  default=PLOTTER, type="string",
                  help="plotting module [default: %default]")
parser.add_option("-v", "--verbose", action="store_true", dest="verbose",
                  default=verbose,
                  help="print debug messages [default: False]")

parser.add_option("--no-plots", action="store_false", dest="plotting",
                  default=plotting,
                  help="suppress the drawing of plots [default: False]")
parser.add_option("--no-predict", action="store_false", dest="predicting",
                  default=predicting,
                  help="don't predict genes, instead treat the input files " +
                  "as predicted genes [default: False]")
parser.add_option("--no-cluster", action="store_false", dest="clustering",
                  default=True, help="don't cluster the sequences, " +
                  "instead treat the input files as alignments " +
                  "[default: False]")
parser.add_option("--no-rename", action="store_false", dest="renaming",
                  default=True,
                  help="don't rename the fasta and clustal files " +
                  "[default: False]")
parser.add_option("--no-reports", action="store_false", dest="reporting",
                  default=True,
                  help="don't generate files for variance data " +
                  "[default: False]")
parser.add_option("--no-calculation", action="store_false",
                  dest="calculating", default=True,
                  help="don't calculate sequence variance [default: False]")


def debug(msg):
    if verbose:
        lock.acquire(True)
        stderr.write(str(msg) + '\n')
        lock.release()


def parse(pargs):
    '''
    Parses `pargs` and sets global variables to be accessible to other
    modules.

    These variables are:
    * `LENGTH_ERR`
    * `MIN_IDENTITY`
    * `MAX_EVALUE`
    * `NUM_THREADS`
    * `NUM_PROCESSES`
    * `START_CODONS`
    * `START_CODONS`
    * `DIRECTORY`
    * `PLOTTER`
    * `args`
    '''
    global \
        LENGTH_ERR, MIN_IDENTITY, MAX_EVALUE, MIN_ORFLEN, \
        NUM_THREADS, NUM_PROCESSES, START_CODONS, STOP_CODONS, \
        DIRECTORY, PLOTTER, args, predicting, clustering, \
        renaming, calculating, reporting, plotting, verbose

    opts, largs = parser.parse_args(pargs)

    if opts.directory[-1] != sep:
        opts.directory += sep
    try:
        makedirs(opts.directory)
    except OSError:
        pass

    if '*' in opts.start:
        DNA = 'ATCG'
        opts.start = set(i + j + k for i in DNA for j in DNA for k in DNA) - \
            set(opts.stop)

    opts.processes = min(opts.processes, len(largs))
    if not (0 <= opts.fraction <= 1):
        raise RuntimeError("Allowable length error must be between 0 and 1.")

    LENGTH_ERR = opts.fraction
    MIN_IDENTITY = opts.identity
    MAX_EVALUE = opts.evalue
    MIN_ORFLEN = opts.orflen
    NUM_THREADS = opts.threads
    NUM_PROCESSES = opts.processes
    STOP_CODONS = opts.stop
    START_CODONS = opts.start
    DIRECTORY = opts.directory
    PLOTTER = opts.plotter

    predicting = opts.predicting
    clustering = opts.clustering
    renaming = opts.renaming
    calculating = opts.calculating
    reporting = opts.reporting
    plotting = opts.plotting

    verbose = opts.verbose

    args = largs


def help():
    '''
    Prints the usage.
    '''
    parser.print_help()