# This code will test out the idea of using kmc to
# 1. quickly enumerate the k-mers
# 2. intersect these with the training database, output as fasta
# 3. use that reduced fasta of intersecting kmers as the query to CMash

####################################################################
# First, I will need to dump the training database to a fasta file
from CMash import MinHash as MH
import os
import blist

training_out_file = '/nfs1/Koslicki_Lab/koslickd/KMC_test/NathanRefSeqTraining60mers.fa'
training_data ='/nfs1/Koslicki_Lab/koslickd/MiCOPCMash/TrainingData/NathanRefSeq/micopdb_n_1000_k_60.h5'
training_file_names = "/nfs1/Koslicki_Lab/koslickd/MiCOPCMash/TrainingData/NathanRefSeq/absolute_file_names.txt"

file_names = []
with open(training_file_names, 'r') as fid:
	iter = 0
	for line in fid.readlines():
		line = line.strip()
		file_names.append(os.path.basename(line))
		iter += 1
		if iter > 1000:
			break

all_kmers = blist.blist()
for file_name in file_names:
	sketch = MH.import_multiple_from_single_hdf5(training_data, import_list=[file_name])[0]
	all_kmers += sketch._kmers

all_kmers_set = set(all_kmers)

with open(training_out_file, 'w') as fid:
	iter = 0
	for kmer in all_kmers_set:
		fid.write(">seq_%d\n" % iter)
		fid.write("%s\n" % kmer)
		iter += 1

##########################################################################


Add file to test out kmc approach. Dump training k-mers to fasta file
Add file to test out kmc approach. Dump training k-mers to fasta file
