def test_inject_seqs(self):
rand_maker = fasta.RandomMaker()
rand_maker.names = [">seq1", ">seq2"]
new_seqs = ["this is new", "also new"]
new_fasta_seqs = rand_maker.inject_seqs(new_seqs)
expected = [">seq1", "this is new", ">seq2", "also new"]
assert new_fasta_seqs == expected
def test_inject_seqs(self):
rand_maker = fasta.RandomMaker()
rand_maker.names = ['>seq1', '>seq2']
new_seqs = ['this is new', 'also new']
new_fasta_seqs = rand_maker.inject_seqs(new_seqs)
expected = ['>seq1', 'this is new', '>seq2', 'also new']
assert new_fasta_seqs == expected
def _run_gen_rand_rnas(in_fasta, out_fasta, kmer, mutations, seed, group):
# Note: This function is separated for testing purposes.
# TODO do something with group?
if seed is not None:
seed = int(seed)
rand_maker = fasta.RandomMaker(in_fasta, out_fasta, kmer, mutations, seed, group)
rand_maker.synthesize_random()
def test_split(self):
rand_maker = fasta.RandomMaker(k=2, seed=1)
seqs = ["this sentence is 35 characters long", "this one is 14"]
rand_maker.seqs = seqs
seq = "TCATTAAGCGCGTCGGTCTCTGTGTACGTCATCTCCATTTTTTTTCGTG"
rand_seqs = rand_maker.split(seq)
expected = ["TCATTAAGCGCGTCGGTCTCTGTGTACGTCATCTC", "CATTTTTTTTCGTG"]
assert rand_seqs == expected
assert len(expected[0]) == 35
assert len(expected[1]) == 14
def test_get_random_seqs(self):
rand_maker = fasta.RandomMaker(k=2, seed=1)
seqs = [
"AGTCAGTCAGTCAGTC", "ATGATATATATATGAT", "ATGCATAGTTTTTTTTTCTGC"
]
rand_seqs = rand_maker.get_random_seqs(seqs)
expected = [
"AGTCAGTCAGTCAGTC", "ATGATGATATATATAT", "ATTGCTTTGTTTAGCATTTTC"
]
assert rand_seqs == expected
def test_synthesize_random(self, tmpdir):
infasta = "tests/data/example.fa"
infasta = pkg_resources.resource_filename("seekr", infasta)
outfasta = str(tmpdir.join("rand.fa"))
rand_maker = fasta.RandomMaker(infasta, outfasta, seed=1)
rand_maker.synthesize_random()
with open(outfasta) as outfasta:
rand_fasta = "".join(next(outfasta) for i in range(6))
expected = ">SEQ1\n" "AAAAAA\n" ">SEQ2\n" "GTGTGTGTGTTG\n" ">SEQ3\n" "ATTACTTGGCACCGGA\n"
assert rand_fasta == expected
def test_split(self):
rand_maker = fasta.RandomMaker(k=2, seed=1)
seqs = [
'this sentence is 35 characters long',
'this one is 14'
]
rand_maker.seqs = seqs
seq = 'TCATTAAGCGCGTCGGTCTCTGTGTACGTCATCTCCATTTTTTTTCGTG'
rand_seqs = rand_maker.split(seq)
expected = ['TCATTAAGCGCGTCGGTCTCTGTGTACGTCATCTC',
'CATTTTTTTTCGTG']
assert rand_seqs == expected
assert len(expected[0]) == 35
assert len(expected[1]) == 14
def test_synthesize_random(self, tmpdir):
infasta = 'tests/data/example.fa'
infasta = pkg_resources.resource_filename('seekr', infasta)
outfasta = str(tmpdir.join('rand.fa'))
rand_maker = fasta.RandomMaker(infasta, outfasta, seed=1)
rand_maker.synthesize_random()
with open(outfasta) as outfasta:
rand_fasta = ''.join(next(outfasta) for i in range(6))
expected = ('>SEQ1\n'
'AAAAAA\n'
'>SEQ2\n'
'GTGTGTGTGTTG\n'
'>SEQ3\n'
'ATTACTTGGCACCGGA\n')
assert rand_fasta == expected
def test_shuffle2(self):
rand_maker = fasta.RandomMaker(k=2, seed=1)
rand_seq = rand_maker.shuffle('AGTCAGTCAGTCAGTC')
assert rand_seq == 'AGTCAGTCAGTCAGTC'
kmer_counts = {
'AA': 0,
'AG': 4,
'AT': 0,
'AC': 0,
'GA': 0,
'GG': 0,
'GT': 4,
'GC': 0,
'TA': 0,
'TG': 0,
'TT': 0,
'TC': 4,
'CA': 3,
'CG': 0,
'CT': 0,
'CC': 0
}
rand_kmer_counts = {k:rand_seq.count(k) for k in kmer_counts}
assert kmer_counts == rand_kmer_counts
def test_shuffle2(self):
rand_maker = fasta.RandomMaker(k=2, seed=1)
rand_seq = rand_maker.shuffle("AGTCAGTCAGTCAGTC")
assert rand_seq == "AGTCAGTCAGTCAGTC"
kmer_counts = {
"AA": 0,
"AG": 4,
"AT": 0,
"AC": 0,
"GA": 0,
"GG": 0,
"GT": 4,
"GC": 0,
"TA": 0,
"TG": 0,
"TT": 0,
"TC": 4,
"CA": 3,
"CG": 0,
"CT": 0,
"CC": 0,
}
rand_kmer_counts = {k: rand_seq.count(k) for k in kmer_counts}
assert kmer_counts == rand_kmer_counts
def test_mutations(self):
rand_maker = fasta.RandomMaker(seed=1)
rand_maker.mutations = 2
rand_seq = rand_maker.shuffle('AAAAAA')
assert rand_seq == 'ACGAAA'
def test_shuffle1(self):
rand_maker = fasta.RandomMaker(seed=1)
rand_seq = rand_maker.shuffle('AGTCAGTC')
assert rand_seq == 'TTGGACAC'