def test_update_primer_hits(self):
'''test _update_primer_hits'''
u = uniqueness.PrimerUniqueness('genomes_file',
'primer3_outdir',
'outprefix',
min_product_length=50,
max_product_length=200)
primer_hits = {}
u._update_primer_hits(primer_hits, {}, 'genome1')
self.assertEqual({}, primer_hits)
pairs_dict = {
'primer1': {
'left': {
'contig1': [(0, 13, False, 'AGTAATTAATAAC')]
},
'right': {
'contig1': [(100, 14, True, 'TCGCTCCAGGTACG')]
}
}
}
u._update_primer_hits(primer_hits, pairs_dict, 'genome2')
expected = {
'primer1': {
'genome2': {
'contig1': [((0, 13, False, 'AGTAATTAATAAC'),
(100, 14, True, 'TCGCTCCAGGTACG'))]
}
}
}
self.assertEqual(expected, primer_hits)
def test_all_primer_matches(self):
'''test _all_primer_matches'''
test_dict = {
'left': {
'contig1': [(0, 10, False, 'ACGTACGTAC'),
(40, 10, True, 'ACGTACGTAC')],
'contig2': [(0, 10, False, 'ACGTACGTAC'),
(1000, 10, False, 'ACGTACGTAC')],
},
'right': {
'contig1': [(40, 10, True, 'ACGTACGTAC')],
'contig2': [(1040, 10, True, 'ACGTACGTAC')],
},
}
u = uniqueness.PrimerUniqueness('genomes_file',
'primer3_outdir',
'outprefix',
min_product_length=50,
max_product_length=200)
got = u._all_primer_matches(test_dict)
expected = {
'contig1':
[((0, 10, False, 'ACGTACGTAC'), (40, 10, True, 'ACGTACGTAC'))],
'contig2':
[((1000, 10, False, 'ACGTACGTAC'), (1040, 10, True, 'ACGTACGTAC'))]
}
self.assertEqual(expected, got)
def test_cat_primer_fastas(self):
'''test _cat_primer_fastas'''
primer3_dir = os.path.join(
data_dir, 'uniqueness_test_cat_primer_fastas.primer3_dir')
names = ['genome1', 'genome2', 'genome3']
genome_files = [
os.path.join(data_dir,
'uniqueness_test_cat_primer_fastas.genome1.fa'),
os.path.join(data_dir,
'uniqueness_test_cat_primer_fastas.genome2.fa'),
os.path.join(data_dir,
'uniqueness_test_cat_primer_fastas.genome3.fa')
]
make_primers = [1, 1, 0]
genomes_file = 'tmp.test.uniqueness_cat_primer_fastas.genomes_file'
write_fake_genomes_file(names, genome_files, make_primers,
genomes_file)
uniq = uniqueness.PrimerUniqueness(genomes_file, primer3_dir,
'outprefix')
genomes = genome_set.GenomeSet(genomes_file)
catted_fasta = 'tmp.test.uniqueness_cat_primer_fastas.out.fa'
uniq._cat_primer_fastas(genomes, catted_fasta)
expected = os.path.join(data_dir,
'uniqueness_test_cat_primer_fastas.out.fa')
self.assertTrue(filecmp.cmp(expected, catted_fasta, shallow=False))
os.unlink(genomes_file)
os.unlink(catted_fasta)
def test_write_all_output_files(self):
'''test _write_all_output_files'''
primer3_dir = os.path.join(
data_dir, 'uniqueness_test_cat_primer_fastas.primer3_dir')
names = ['genome1', 'genome2', 'genome3']
genome_files = [
os.path.join(data_dir,
'uniqueness_test_cat_primer_fastas.genome1.fa'),
os.path.join(data_dir,
'uniqueness_test_cat_primer_fastas.genome2.fa'),
os.path.join(data_dir,
'uniqueness_test_cat_primer_fastas.genome3.fa')
]
make_primers = [1, 1, 0]
genomes_file = 'tmp.test.uniqueness_cat_primer_fastas.genomes_file'
write_fake_genomes_file(names, genome_files, make_primers,
genomes_file)
uniq = uniqueness.PrimerUniqueness(genomes_file, primer3_dir,
'tmp.test_write_all_output_files')
genomes = genome_set.GenomeSet(genomes_file)
primer_hits = {
'primer1': {
'genome2': {
'contig1': [((0, 13, False, 'AGTAATTAATAAC'),
(100, 14, True, 'TCGCTCCAGGTACG'))]
}
},
'primer2': {
'genome1': {
'contig1': [((0, 13, False, 'AGTAATTAATAAC'),
(100, 14, True, 'TCGCTCCAGGTACG'))]
},
'genome2': {
'contig2': [((10, 23, False, 'AGTAATTAATAAC'),
(110, 24, True, 'TCGCTCCAGGTACG'))]
}
}
}
uniq._write_all_output_files(primer_hits, genomes)
for suffix in ('all_primers.hits.tsv', 'genome_uniqueness.tsv',
'unique_primers.tsv'):
got = 'tmp.test_write_all_output_files.' + suffix
expected = os.path.join(
data_dir,
'uniqueness_test_write_all_output_files.expected.' + suffix)
self.assertTrue(filecmp.cmp(got, expected, shallow=False))
os.unlink(got)
os.unlink(genomes_file)
def test_good_primer_pairs_from_lists(self):
'''test _good_primer_pairs_from_lists'''
p1 = (0, 10, False, 'ACGTACGTAC')
p2 = (30, 10, False, 'ACGTACGTAC')
p3 = (40, 10, True, 'ACGTACGTAC')
p4 = (35, 10, True, 'ACGTACGTAC')
p5 = (1000, 10, False, 'ACGTACGTAC')
p6 = (1040, 10, True, 'ACGTACGTAC')
list1 = [p1, p5]
list2 = [p2, p3, p4, p6]
expected = [(p1, p3), (p5, p6)]
u = uniqueness.PrimerUniqueness('genomes_file',
'primer3_outdir',
'outprefix',
min_product_length=50,
max_product_length=200)
got = u._good_primer_pairs_from_lists(list1, list2)
self.assertEqual(expected, got)
def test_is_good_primer_pair(self):
'''test _is_good_primer_pair'''
tests = [
[
False, (0, 10, False, 'ACGTACGTAC'),
(30, 10, False, 'ACGTACGTAC')
], # wrong orientation
[False, (0, 10, True, 'ACGTACGTAC'),
(30, 10, True, 'ACGTACGTAC')], # wrong orientation
[
False, (0, 10, False, 'ACGTACGTAC'),
(30, 10, True, 'ACGTACGTAC')
], # wrong orientation
[
False, (0, 10, False, 'ACGTACGTAC'),
(39, 10, True, 'ACGTACGTAC')
], # too short
[
False, (0, 10, False, 'ACGTACGTAC'),
(500, 10, True, 'ACGTACGTAC')
], # too long
[
False, (39, 10, True, 'ACGTACGTAC'),
(0, 10, False, 'ACGTACGTAC')
], # too short
[
False, (30, 10, False, 'ACGTACGTAC'),
(0, 10, True, 'ACGTACGTAC')
], # wrong order
[True, (0, 10, False, 'ACGTACGTAC'), (40, 10, True, 'ACGTACGTAC')],
[True, (40, 10, True, 'ACGTACGTAC'), (0, 10, False, 'ACGTACGTAC')],
]
for expected, left_primer, right_primer in tests:
u = uniqueness.PrimerUniqueness('genomes_file',
'primer3_outdir',
'outprefix',
min_product_length=50,
max_product_length=200)
self.assertEqual(expected,
u._is_good_primer_pair(left_primer, right_primer))