#! /usr/bin/env python
"""
"""

import khmer, sys
import os.path

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

def main():
    parser = build_construct_args()
    parser.add_argument('--build-tagset', '-t', default=True,
                        action='store_false',
                        help='Construct tagset while loading sequences')
    parser.add_argument('input_contigs')
    parser.add_argument('input_reads', nargs='+')

    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 / 8)' % (args.n_hashes * args.min_hashsize / 8.)
        print>>sys.stderr, '-'*8

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

    base = args.input_contigs
    filenames = args.input_reads

    ###
    
    print 'making hashtable'
    ht = khmer.new_hashbits(K, HT_SIZE, N_HT)

    for filename in filenames:
       print 'consuming input', filename
       ht.consume_fasta(filename)

    ###

    print 'reading contigs from', args.input_contigs

    fp = open(os.path.basename(args.input_contigs) + '.unfound', 'w')

    for contig in screed.open(base):
        seq = contig.sequence
        
        n_not_found = 0
        found = True
        for start in range(0, len(seq) - K):
            kmer = seq[start:start + K]
            if not ht.get(kmer):
                n_not_found += 1
                found = False

        if not found:
            fp.write('>%s %d %d\n%s\n' % (contig.name, n_not_found, len(contig.sequence), contig.sequence))

if __name__ == '__main__':
    main()