import sys, khmer
import os.path
import screed

K=20

readsfile = sys.argv[1]
contigfile = sys.argv[2]
outfile = os.path.basename(readsfile) + '.sweep'
if len(sys.argv) == 4:
    outfile = sys.argv[3]

# create a hashbits data structure
ht = khmer.new_hashbits(K, 1, 1)

# tag every k-mer in the contigs
ht._set_tag_density(0)

# load contigs, connect into N partitions
print 'loading contigs from', contigfile
ht.consume_fasta_and_tag(contigfile)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)

print 'outputting contig-partitioned reads to', outfile
ht.output_partitions(readsfile, outfile, True)