def test_build_exon_overlap_cluster_with_lnc_in_intron(self):
# read1: ++++....................++++
# read2: ++++....++++
read1 = make_read(0, "read1", 100, [(0, 100), (3, 500), (0, 100)])
read2 = make_read(0, "read2", 300, [(0, 100), (3, 100), (0, 100)])
read_list = [read1, read2]
clusterlist = GeneLinkageFinder.build_exon_overlap_cluster(read_list)
self.assertEqual(len(clusterlist), 2)
def test_split_cluster_by_overlap_with_same_cluster(self):
# read1: ++++....++++
# read2: ++++....+
# read3: ++++....++++....++++
read1 = make_read(0, "read1", 100, [(0, 100), (3, 100), (0, 100)])
read2 = make_read(0, "read2", 100, [(0, 100), (3, 100), (0, 10)])
read3 = make_read(0, "read3", 100, [(0, 100), (3, 100), (0, 100),
(3, 100), (0, 100)])
cluster = [read1, read2, read3]
clusterlist = GeneLinkageFinder.split_cluster_by_overlap(cluster)
self.assertEqual(len(clusterlist), 1)
def test_build_exon_overlap_cluster_with_no_overlap_iso(self):
# read1: ++++....++++
# read2: ++++....+
# read3: ++++....++++....++++
read1 = make_read(0, "read1", 100, [(0, 100), (3, 100), (0, 100)])
read2 = make_read(0, "read2", 600, [(0, 100), (3, 100), (0, 10)])
read3 = make_read(0, "read3", 100, [(0, 100), (3, 100), (0, 100),
(3, 100), (0, 100)])
read_list = [read1, read2, read3]
clusterlist = GeneLinkageFinder.build_exon_overlap_cluster(read_list)
self.assertEqual(len(clusterlist), 2)
def test_filter_cluster_by_strand_with_diff_intron(self):
# read1: ++++....++++
# read2: ----....-
read1 = make_read(0, "read1", 100, [(0, 100), (3, 100), (0, 100)])
read2 = make_read(0, "read2", 150, [(0, 100), (3, 100), (0, 10)])
read2.is_reverse = True
read1.setTag("FL", 100)
read2.setTag("FL", 1000)
clusterlist = [[read1], [read2]]
res = GeneLinkageFinder.filter_cluster_by_strand(clusterlist)
self.assertEqual(len(res), 2)
def test_build_exon_overlap_cluster_with_diff_strand(self):
# read1: ++++....++++
# read2: ----....-
# read3: ++++....++++....++++
read1 = make_read(0, "read1", 100, [(0, 100), (3, 100), (0, 100)])
read2 = make_read(0, "read2", 100, [(0, 100), (3, 100), (0, 10)])
read3 = make_read(0, "read3", 100, [(0, 100), (3, 100), (0, 100),
(3, 100), (0, 100)])
read2.is_reverse = True
read_list = [read1, read2, read3]
clusterlist = GeneLinkageFinder.build_exon_overlap_cluster(read_list)
self.assertEqual(len(clusterlist), 2)
def test_filter_cluster_by_strand_both_without_intron_1(self):
# read1: ++++
# read2: ----
read1 = make_read(0, "read1", 100, [(0, 100)])
read2 = make_read(0, "read2", 100, [(0, 100)])
read2.is_reverse = True
read1.setTag("FL", 1000)
read2.setTag("FL", 100)
clusterlist = [[read1], [read2]]
res = GeneLinkageFinder.filter_cluster_by_strand(clusterlist)
self.assertEqual(len(res), 1)
self.assertFalse(res[0][0].is_reverse)
def test_find_junction(self):
read = make_read(0, "test", 100, [(0, 20), (3, 20), (0, 20), (1, 1),
(3, 20), (0, 20), (2, 10), (0, 5),
(3, 20), (0, 20)])
junctions = JunctionGraph._find_junction(read, 10)
self.assertEqual(len(junctions), 1)
self.assertEqual(junctions[0],
(("chr1", 120, '+', 'EI'), ("chr1", 140, '+', 'IE')))
def test_adjust_intron_position(self):
read = make_read(0, "test", 100, [(0, 100), (3, 100), (0, 100)])
intron = Intron(read.reference_name, 190, 310, "+")
ElementDiscover.adjust_intron_position(read, intron)
self.assertListEqual(read.blocks, [(100, 190), (310, 400)])
read = make_read(0, "test", 100, [(0, 100), (3, 100), (0, 100)])
intron = Intron(read.reference_name, 210, 290, "+")
ElementDiscover.adjust_intron_position(read, intron)
self.assertListEqual(read.blocks, [(100, 210), (290, 400)])
# Difference chrom
read = make_read(0, "test", 100, [(0, 100), (3, 100), (0, 100)])
intron = Intron("DiffChrom", 190, 310, "+")
ElementDiscover.adjust_intron_position(read, intron)
self.assertListEqual(read.blocks, [(100, 200), (300, 400)])
# Difference strand
read = make_read(0, "test", 100, [(0, 100), (3, 100), (0, 100)])
intron = Intron("DiffChrom", 190, 310, "-")
ElementDiscover.adjust_intron_position(read, intron)
self.assertListEqual(read.blocks, [(100, 200), (300, 400)])
def test_blocks2cigar(self):
blocks = ((0, 20), (3, 80), (0, 75), (3, 42), (0, 30))
read = make_read(0, "test", 100, blocks)
self.assertEqual(ElementDiscover.blocks2cigar(read.blocks), blocks)