import sys, screed.fasta, os
import khmer
from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter

MAX_SODD=3

WORKER_THREADS=8
GROUPSIZE=100

###

def main():
    htfile = sys.argv[1]
    outfiles = sys.argv[2:]
        
    print 'loading hashbits'
    ht = khmer.load_hashbits(htfile)

    def process_fn(record, ht=ht):
        name = record['name']
        seq = record['sequence']
        if 'N' in seq:
            return None, None

        trim_seq, trim_at = ht.trim_on_sodd(seq, MAX_SODD)

        if trim_at >= ht.ksize():
            return name, trim_seq

        return None, None

    for filename in outfiles:
       outpath = os.path.basename(filename) + '.sodd'
       outfp = open(outpath, 'w')

       tsp = ThreadedSequenceProcessor(process_fn, WORKER_THREADS, GROUPSIZE)
       tsp.start(verbose_fasta_iter(filename), outfp)

if __name__ == '__main__':
    main()