def test_split_transfrag():
loci = read_gtf("splice_sites.gtf")
interval, gtf_lines = loci[0]
t_dict = Transfrag.parse_gtf(gtf_lines)
sg = SpliceGraph.create(t_dict.values())
boundaries = array("i", sg._find_node_boundaries())
# check nodes
t = t_dict["A"]
nodes = tuple(split_transfrag(t, boundaries))
assert nodes == ((10, 100), (200, 250), (250, 300), (400, 525))
t = t_dict["B"]
nodes = tuple(split_transfrag(t, boundaries))
assert nodes == ((10, 100), (250, 300), (400, 525))
t = t_dict["C"]
nodes = tuple(split_transfrag(t, boundaries))
assert nodes == ((150, 200), (200, 250), (250, 300), (400, 525))
t = t_dict["D"]
nodes = tuple(split_transfrag(t, boundaries))
assert nodes == ((375, 400), (400, 525))
def test_split_transfrag():
loci = read_gtf('splice_sites.gtf')
interval, gtf_lines = loci[0]
t_dict = Transfrag.parse_gtf(gtf_lines)
sg = SpliceGraph.create(t_dict.values())
boundaries = array('i', sg._find_node_boundaries())
# check nodes
t = t_dict['A']
nodes = tuple(split_transfrag(t, boundaries))
assert nodes == ((10, 100), (200, 250), (250, 300), (400, 525))
t = t_dict['B']
nodes = tuple(split_transfrag(t, boundaries))
assert nodes == ((10, 100), (250, 300), (400, 525))
t = t_dict['C']
nodes = tuple(split_transfrag(t, boundaries))
assert nodes == ((150, 200), (200, 250), (250, 300), (400, 525))
t = t_dict['D']
nodes = tuple(split_transfrag(t, boundaries))
assert nodes == ((375, 400), (400, 525))
def test_create_locus():
loci = read_gtf('splice_sites.gtf')
assert len(loci) == 1
interval, gtf_lines = loci[0]
assert interval == ('chr1', 10, 525)
t_dict = Transfrag.parse_gtf(gtf_lines)
locus = Locus.create(t_dict.values())
assert locus.chrom == 'chr1'
assert locus.start == 10
assert locus.end == 525
a = locus.get_expr_data(49, 51, Strand.POS)
assert np.array_equal(a, [1.0, 2.0])
a = locus.get_expr_data(150, 151, Strand.POS)
assert np.array_equal(a, [1.0])
a = locus.get_expr_data(499, 501, Strand.POS)
assert np.array_equal(a, [3.0, 1.0])
with pytest.raises(TacoError):
locus.get_expr_data(5, 15, Strand.POS)
with pytest.raises(TacoError):
locus.get_expr_data(520, 530, Strand.POS)
def test_parse_loci():
loci = read_gtf('parse_loci.gtf')
assert len(loci) == 3
assert loci[0][0] == ('chr1', 10, 50)
assert loci[1][0] == ('chr1', 50, 200)
assert loci[2][0] == ('chr2', 100, 200)
def test_multi_strand1():
# read gtf and test basic values
loci = read_gtf("multi_strand1.gtf")
assert len(loci) == 1
interval, gtf_lines = loci[0]
assert interval == ("chr1", 100, 1000)
t_dict = Transfrag.parse_gtf(gtf_lines)
assert len(t_dict) == 5
locus = Locus.create(t_dict.values())
assert locus.chrom == "chr1"
assert locus.start == 100
assert locus.end == 1000
# raise exception when creating with multiple strands
with pytest.raises(TacoError):
SpliceGraph.create(t_dict.values())
transfrags_pos = locus.get_transfrags(Strand.POS)
transfrags_neg = locus.get_transfrags(Strand.NEG)
sgpos = SpliceGraph.create(transfrags_pos)
sgneg = SpliceGraph.create(transfrags_neg)
# test
assert sgpos.chrom == "chr1"
assert sgpos.start == 100
assert sgpos.end == 650
assert sgpos.strand == Strand.POS
assert sgpos.ref_start_sites == [150]
assert sgpos.ref_stop_sites == [600]
with pytest.raises(TacoError):
sgpos.get_expr_data(90, 110)
with pytest.raises(TacoError):
sgpos.get_expr_data(650, 655)
assert np.array_equal(sgpos.get_expr_data(100, 105), np.ones(5))
assert sgneg.chrom == "chr1"
assert sgneg.start == 350
assert sgneg.end == 1000
assert sgneg.strand == Strand.NEG
assert sgneg.ref_start_sites == [1000]
assert sgneg.ref_stop_sites == [350]
with pytest.raises(TacoError):
sgneg.get_expr_data(340, 350)
with pytest.raises(TacoError):
sgneg.get_expr_data(1000, 1010)
assert np.array_equal(sgneg.get_expr_data(400, 405), np.ones(5))
assert np.array_equal(sgneg.get_expr_data(945, 950), np.zeros(5))
assert np.array_equal(sgneg.get_expr_data(950, 955), np.ones(5))
assert np.array_equal(sgneg.get_expr_data(980, 985), np.zeros(5))
# test locus boundaries
bpos = tuple(sgpos._find_node_boundaries())
assert bpos == tuple((100, 200, 300, 400, 650))
bneg = tuple(sgneg._find_node_boundaries())
assert bneg == tuple((350, 400, 500, 950, 980, 1000))
# added guided ends/assembly to use boundaries from reference
lpos = SpliceGraph.create(transfrags_pos, guided_ends=True, guided_assembly=True)
bpos = tuple(lpos._find_node_boundaries())
assert bpos == tuple((100, 150, 200, 300, 400, 500, 600, 650))
lneg = SpliceGraph.create(transfrags_neg, guided_ends=True, guided_assembly=True)
bneg = tuple(lneg._find_node_boundaries())
assert bneg == tuple((350, 400, 500, 750, 900, 950, 980, 1000))
def test_multi_strand1():
# read gtf and test basic values
loci = read_gtf('multi_strand1.gtf')
assert len(loci) == 1
interval, gtf_lines = loci[0]
assert interval == ('chr1', 100, 1000)
t_dict = Transfrag.parse_gtf(gtf_lines)
assert len(t_dict) == 5
locus = Locus.create(t_dict.values())
assert locus.chrom == 'chr1'
assert locus.start == 100
assert locus.end == 1000
# raise exception when creating with multiple strands
with pytest.raises(TacoError):
SpliceGraph.create(t_dict.values())
transfrags_pos = locus.get_transfrags(Strand.POS)
transfrags_neg = locus.get_transfrags(Strand.NEG)
sgpos = SpliceGraph.create(transfrags_pos)
sgneg = SpliceGraph.create(transfrags_neg)
# test
assert sgpos.chrom == 'chr1'
assert sgpos.start == 100
assert sgpos.end == 650
assert sgpos.strand == Strand.POS
assert sgpos.ref_start_sites == [150]
assert sgpos.ref_stop_sites == [600]
with pytest.raises(TacoError):
sgpos.get_expr_data(90, 110)
with pytest.raises(TacoError):
sgpos.get_expr_data(650, 655)
assert np.array_equal(sgpos.get_expr_data(100, 105), np.ones(5))
assert sgneg.chrom == 'chr1'
assert sgneg.start == 350
assert sgneg.end == 1000
assert sgneg.strand == Strand.NEG
assert sgneg.ref_start_sites == [1000]
assert sgneg.ref_stop_sites == [350]
with pytest.raises(TacoError):
sgneg.get_expr_data(340, 350)
with pytest.raises(TacoError):
sgneg.get_expr_data(1000, 1010)
assert np.array_equal(sgneg.get_expr_data(400, 405), np.ones(5))
assert np.array_equal(sgneg.get_expr_data(945, 950), np.zeros(5))
assert np.array_equal(sgneg.get_expr_data(950, 955), np.ones(5))
assert np.array_equal(sgneg.get_expr_data(980, 985), np.zeros(5))
# test locus boundaries
bpos = tuple(sgpos._find_node_boundaries())
assert bpos == tuple((100, 200, 300, 400, 650))
bneg = tuple(sgneg._find_node_boundaries())
assert bneg == tuple((350, 400, 500, 950, 980, 1000))
# added guided ends/assembly to use boundaries from reference
lpos = SpliceGraph.create(transfrags_pos,
guided_ends=True,
guided_assembly=True)
bpos = tuple(lpos._find_node_boundaries())
assert bpos == tuple((100, 150, 200, 300, 400, 500, 600, 650))
lneg = SpliceGraph.create(transfrags_neg,
guided_ends=True,
guided_assembly=True)
bneg = tuple(lneg._find_node_boundaries())
assert bneg == tuple((350, 400, 500, 750, 900, 950, 980, 1000))
