def test_shift(seq):
import numpy as np
shifted = np.array([
kmers.kmers(seq[i:i + KMER_SIZE].encode('ascii'), KMER_SIZE)[0]
for i in range(len(seq) - KMER_SIZE + 1)
])
fast = kmers.kmers(seq.encode('ascii'), KMER_SIZE)
assert len(shifted) == len(fast)
assert np.all(shifted == fast)
def test_kmers():
testing = 'ATTTAACATGAGATAACATGCATGCATGCATTGCGGCTCAGCTAGTCAGCTAGCTAGCTAGCTACGATCGATCGTAGCATCGATCGATCGATCGATCGATCGATCGTACGTACGTAGCTACGATCGTAGCTAGCTAG'
testing = testing.encode('ascii')
print(kmers.kmers(testing, KMER_SIZE))
testing = 'TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'
testing = testing.encode('ascii')
print(kmers.kmers(testing, KMER_SIZE))
def test_extended_IUPAC_alphabet(seq):
import numpy as np
n = np.array([
encode_kmer_min(seq[i:i + KMER_SIZE])
for i in range(len(seq) - KMER_SIZE + 1)
])
fast = kmers.kmers(seq.encode('ascii'), KMER_SIZE)
assert len(n) == len(fast)
assert np.all(n == fast)
def test_error_detection():
testing = 'ATTTAACATGAGXTAACATGCATGCATGCAT'
testing = testing.encode('ascii')
assert kmers.kmers(testing, KMER_SIZE) is None