def test_get_ligation_structure_biases(self):
sam_file1 = os.path.join(self.dir, "test_matrix",
"yeast.sample.chrI.1_sorted.sam")
sam_file2 = os.path.join(self.dir, "test_matrix",
"yeast.sample.chrI.2_sorted.sam")
chrI = Chromosome.from_fasta(
os.path.join(self.dir, "test_matrix", "chrI.fa"))
genome = Genome(chromosomes=[chrI])
pairs = self.pairs_class()
regions = genome.get_regions('HindIII')
pairs.add_regions(regions.regions)
pair_generator = SamBamReadPairGenerator(sam_file1, sam_file2)
pairs.add_read_pairs(pair_generator)
genome.close()
regions.close()
x, i, o, b = pairs.get_ligation_structure_biases(
sampling=200, skip_self_ligations=False)
assert len(x) == len(i) == len(o) == len(b) == 3
assert x.tolist() == [470, 4489, 19259]
assert i.tolist() == [
2.8756218905472637, 0.8059701492537313, 0.6368159203980099
]
assert o.tolist() == [
0.2537313432835821, 0.24875621890547264, 0.46766169154228854
]
assert b.tolist() == [830, 413, 423]
pairs.close()
def test_from_pairs(self):
sam_file1 = os.path.join(self.dir, "test_matrix",
"yeast.sample.chrI.1_sorted.sam")
sam_file2 = os.path.join(self.dir, "test_matrix",
"yeast.sample.chrI.2_sorted.sam")
chrI = Chromosome.from_fasta(
os.path.join(self.dir, "test_matrix", "chrI.fa"))
genome = Genome(chromosomes=[chrI])
pairs = ReadPairs()
regions = genome.get_regions('HindIII')
pairs.add_regions(regions)
g = SamBamReadPairGenerator(sam_file1, sam_file2)
pairs.add_read_pairs(g)
genome.close()
regions.close()
pl = len(pairs)
hic = pairs.to_hic(_hic_class=self.hic_class)
assert len(hic.regions) == len(pairs.regions)
pairs.close()
reads = 0
edge_set = set()
for edge in hic.edges():
key = (edge.source, edge.sink)
assert key not in edge_set
edge_set.add(key)
reads += edge.weight
assert reads == pl
hic.close()
def setup_method(self, method):
chr1 = Chromosome(name='chr1',
length=10000,
sequence='agcgctgctgaagcttcgatcgtaagcttc')
chr2 = Chromosome(name='chr2',
length=5000,
sequence='gcgctgctgaagcttcgatcgtaagcttc')
self.genome = Genome(chromosomes=[chr1, chr2])
def test_from_string(self):
dir = os.path.dirname(os.path.realpath(__file__))
genome = Genome.from_string(dir + '/test_regions/chromosomes.fa')
chr1 = genome[0]
assert len(chr1) == 5
chr2 = genome[1]
assert len(chr2) == 3
chr3 = genome[2]
assert len(chr3) == 4
chr4 = genome[3]
assert len(chr4) == 2
genome.close()
def test_knight_matrix_balancing_per_chromosome(self):
chrI = Chromosome.from_fasta(self.dir + "/test_matrix/chrI.fa")
genome = Genome(chromosomes=[chrI])
hic = self.hic_class()
regions = genome.get_regions(10000)
genome.close()
hic.add_regions(regions)
regions.close()
hic.load_from_hic(self.hic_cerevisiae)
m = hic[:, :]
assert is_symmetric(m)
kr_balancing(hic, whole_matrix=False)
m_corr = hic[:, :]
assert is_symmetric(m_corr)
for n in sum(m_corr):
if np.ma.is_masked(n):
continue
assert abs(1.0 - n) < 1e-5 or n == 0
hic.close()
def setup_method(self, method):
self.dir = os.path.dirname(os.path.realpath(__file__))
sam1_file = os.path.join(self.dir, "test_pairs",
"lambda_reads1_sort.sam")
sam2_file = os.path.join(self.dir, "test_pairs",
"lambda_reads2_sort.sam")
pair_generator = SamBamReadPairGenerator(sam1_file, sam2_file)
self.pairs = ReadPairs()
self.genome = Genome.from_folder(
os.path.join(self.dir, "test_pairs", "lambda_genome"))
regions = self.genome.get_regions(1000)
self.pairs.add_regions(regions.regions)
regions.close()
self.pairs.add_read_pairs(pair_generator)
self.pairs_class = ReadPairs
def test_ice_matrix_balancing(self):
chrI = Chromosome.from_fasta(self.dir + "/test_matrix/chrI.fa")
genome = Genome(chromosomes=[chrI])
hic = self.hic_class()
regions = genome.get_regions(10000)
genome.close()
hic.add_regions(regions)
regions.close()
hic.load_from_hic(self.hic_cerevisiae)
m = hic[:, :]
assert is_symmetric(m)
ice_balancing(hic)
m_corr = hic[:, :]
assert is_symmetric(m_corr)
sum_m_corr = sum(m_corr)
for n in sum_m_corr:
if np.ma.is_masked(n):
continue
assert (sum_m_corr[0] - 5 < n < sum_m_corr[0] + 5) or n == 0
hic.close()
class TestGenome:
def setup_method(self, method):
chr1 = Chromosome(name='chr1',
length=10000,
sequence='agcgctgctgaagcttcgatcgtaagcttc')
chr2 = Chromosome(name='chr2',
length=5000,
sequence='gcgctgctgaagcttcgatcgtaagcttc')
self.genome = Genome(chromosomes=[chr1, chr2])
def teardown_method(self, method):
self.genome.close()
def test_iter(self):
i = 0
for chromosome in self.genome:
if i == 0:
assert chromosome.name == 'chr1'
assert chromosome.length == 10000
assert chromosome.sequence == 'agcgctgctgaagcttcgatcgtaagcttc'
if i == 1:
assert chromosome.name == 'chr2'
assert chromosome.length == 5000
assert chromosome.sequence == 'gcgctgctgaagcttcgatcgtaagcttc'
i += 1
def test_node_list(self):
regions = self.genome.get_regions('HindIII')
assert len(regions) == 6
for i in range(0, len(regions)):
region = regions[i]
if i == 0:
assert region.chromosome == 'chr1'
assert region.start == 1
assert region.end == 12
if i == 5:
assert region.chromosome == 'chr2'
assert region.start == 25
assert region.end == 5000
i += 1
regions.close()
nl = self.genome.get_regions(4000)
assert len(nl) == 5
for i in range(0, len(nl)):
node = nl[i]
if i == 0:
assert node.chromosome == 'chr1'
assert node.start == 1
assert node.end == 4000
if i == 5:
assert node.chromosome == 'chr2'
assert node.start == 4001
assert node.end == 5000
i += 1
nl.close()
def test_from_string(self):
dir = os.path.dirname(os.path.realpath(__file__))
genome = Genome.from_string(dir + '/test_regions/chromosomes.fa')
chr1 = genome[0]
assert len(chr1) == 5
chr2 = genome[1]
assert len(chr2) == 3
chr3 = genome[2]
assert len(chr3) == 4
chr4 = genome[3]
assert len(chr4) == 2
genome.close()