# /usr/bin/env python
"""
@@
"""

import sys, screed
import khmer
from khmer.counting_args import build_construct_args, DEFAULT_MIN_HASHSIZE

DEFAULT_LOWER_CUTOFF=2000
DEFAULT_UPPER_CUTOFF=65535

###

def main():
    parser = build_construct_args()
    parser.add_argument('-l', '--lower-cutoff', type=int, dest='lower_cutoff',
                        default=DEFAULT_LOWER_CUTOFF)
    parser.add_argument('-u', '--upper-cutoff', type=int, dest='upper_cutoff',
                        default=DEFAULT_UPPER_CUTOFF)
    
    parser.add_argument('output_filename')
    parser.add_argument('input_filename')

    args = parser.parse_args()

    if not args.quiet:
        if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
            print>>sys.stderr, "** WARNING: hashsize is default!  You absodefly want to increase this!\n** Please read the docs!"

        print>>sys.stderr, '\nPARAMETERS:'
        print>>sys.stderr, ' - kmer size =    %d \t\t(-k)' % args.ksize
        print>>sys.stderr, ' - n hashes =     %d \t\t(-N)' % args.n_hashes
        print>>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % args.min_hashsize
        print>>sys.stderr, ''
        print>>sys.stderr, 'Estimated memory usage is %.2g bytes (n_hashes x min_hashsize)' % (args.n_hashes * args.min_hashsize)
        print>>sys.stderr, '-'*8


    K=args.ksize
    HT_SIZE=args.min_hashsize
    N_HT=args.n_hashes

    output = args.output_filename
    input = args.input_filename

    print 'lower cutoff:', args.lower_cutoff
    print 'upper cutoff:', args.upper_cutoff
    print 'Saving stoptags to %s' % output
    print 'Loading sequences in %s' % input

    ###
    
    print 'making hashtable'
    ht = khmer.new_counting_hash(K, HT_SIZE, N_HT)
    ht.set_use_bigcount(True)

    print 'consuming input', input
    hb = ht.collect_high_abundance_kmers(input,
                                         args.lower_cutoff,
                                         args.upper_cutoff)

    print 'saving stoptags', output
    hb.save_stop_tags(output)
    
if __name__ == '__main__':
    main()