def test_build_contig_db_from_fasta(self):
conn = sqlite3.connect(':memory:')
ramifier = RotatingRamifier.from_file(4, KMER_ROTATION)
contig_db = ContigDB(conn, ramifier=ramifier, box_side_len=0.5)
contig_db.fast_add_kmers_from_fasta(KMER_FASTA)
contig_db.commit()
stored = contig_db.get_all_contigs()
self.assertGreaterEqual(len(stored), 3)
def build_contig_cover_fasta(radius, dimension, threads, outfile, rotation,
fasta_list):
environ[
'OPENBLAS_NUM_THREADS'] = f'{threads}' # numpy uses one of these two libraries
environ['MKL_NUM_THREADS'] = f'{threads}'
fasta_list = [line.strip() for line in fasta_list]
ramifier = RotatingRamifier.from_file(dimension, rotation)
grid = ContigDB(sqlite3.connect(outfile),
ramifier=ramifier,
box_side_len=radius)
click.echo(f'Adding {len(fasta_list)} fastas.', err=True)
start = time()
with click.progressbar(fasta_list) as fastas:
for fasta_filename in fastas:
n_added = grid.fast_add_kmers_from_fasta(fasta_filename)
grid.close()
add_time = time() - start
click.echo(f'Added {n_added:,} kmers to {outfile} in {add_time:.5}s. ',
err=True)