# SeqMap
# Seq workshop -- Section 2
# Reads and constructs a hash table index from an input
# FASTA file.
# Usage: seqc run section2.seq <FASTA path>
from sys import argv
from bio import *
import pickle
import gzip

index = {}

for record in FASTA(argv[1]):
    for pos,kmer in record.seq.kmers_with_pos(k=32, step=1):
        index[min(kmer, ~kmer)] = pos

with gzip.open(argv[1] + '.index', 'wb') as jar:
    pickle.dump(index, jar)