def test_set_type_of_5_prime_tss(self):
self.tss_gene_mapper.genes_and_5_prime_tss = {}
self.tss_gene_mapper.tss_and_hit_genes = {}
tss_primary = TSS("genomeX", 40, "+")
tss_secondary = TSS("genomeX", 30, "+")
gene = Gene("genomeX", "g", "g", 50, 100, "+")
self.tss_gene_mapper.genes_and_5_prime_tss[gene] = [[10, tss_primary],
[
20,
tss_secondary
]]
self.tss_gene_mapper.tss_and_hit_genes[tss_primary] = {}
self.tss_gene_mapper.tss_and_hit_genes[tss_secondary] = {}
self.tss_gene_mapper.tss_and_hit_genes[tss_primary][gene] = {
"location": tssgenemapper.loc_5_prime_str,
"orientation": tssgenemapper.sense_str,
"distance": 10,
"tss_type": None
}
self.tss_gene_mapper.tss_and_hit_genes[tss_secondary][gene] = {
"location": tssgenemapper.loc_5_prime_str,
"orientation": tssgenemapper.sense_str,
"distance": 20,
"tss_type": None
}
self.tss_gene_mapper._set_type_of_5_prime_tss()
self.assertEqual(
self.tss_gene_mapper.tss_and_hit_genes[tss_primary][gene]
["tss_type"], tssgenemapper.primary_str)
self.assertEqual(
self.tss_gene_mapper.tss_and_hit_genes[tss_secondary][gene]
["tss_type"], tssgenemapper.secondary_str)
def create_tss_list(self):
self.tss_list = []
for row in csv.reader(self.tss_list_fh, delimiter="\t"):
seq_id = None
if len(row) == 3:
seq_id == row[2]
try:
self.tss_list.append(TSS(seq_id, row[0], row[1]))
except:
sys.stderr.write("Skipping TSS table line: \"%s\"\n" %
("\t".join(row)))
def test_has_5_prime_association_9(self):
"""True - In 5' region"""
tss = TSS("genomeX", 105, "-")
gene = Gene("genomeX", "g", "g", 10, 100, "-")
self.assertEqual(
self.tss_gene_mapper._has_5_prime_association(tss, gene), True)
def test_has_5_prime_association_8(self):
"""None - antisense"""
tss = TSS("genomeX", 600, "+")
gene = Gene("genomeX", "g", "g", 10, 100, "-")
self.assertEqual(
self.tss_gene_mapper._has_5_prime_association(tss, gene), None)
def test_has_5_prime_association_4(self):
"""None - in 5' but too far away """
tss = TSS("genomeX", 10, "+")
gene = Gene("genomeX", "g", "g", 1000, 1100, "+")
self.assertEqual(
self.tss_gene_mapper._has_5_prime_association(tss, gene), None)
def test_has_5_prime_association_3(self):
"""True - Leaderless TSS"""
tss = TSS("genomeX", 10, "+")
gene = Gene("genomeX", "g", "g", 10, 100, "+")
self.assertEqual(
self.tss_gene_mapper._has_5_prime_association(tss, gene), True)
def test_5_prime_dist_4(self):
tss = TSS("genomeX", 120, "-")
gene = Gene("genomeX", "g", "g", 10, 100, "-")
self.assertEqual(self.tss_gene_mapper._5_prime_dist(tss, gene), 20)
def test_init_without_extra(self):
tss = TSS("plasmidX", "20", "-")
self.assertEqual(tss.seq_id, "plasmidX")
self.assertEqual(tss.pos, 20)
self.assertEqual(tss.strand, "-")
self.assertFalse(hasattr(tss, "extra"))
def test_has_internal_association_7(self):
"""True - on the last base """
tss = TSS("genomeX", 10, "-")
gene = Gene("genomeX", "g", "g", 10, 100, "-")
self.assertEqual(
self.tss_gene_mapper._has_internal_association(tss, gene), True)
def test_has_internal_association_3(self):
"""None - 3' region """
tss = TSS("genomeX", 150, "+")
gene = Gene("genomeX", "g", "g", 10, 100, "+")
self.assertEqual(
self.tss_gene_mapper._has_internal_association(tss, gene), None)
def test_has_internal_association_1(self):
"""True - internal"""
tss = TSS("genomeX", 20, "+")
gene = Gene("genomeX", "g", "g", 10, 100, "+")
self.assertEqual(
self.tss_gene_mapper._has_internal_association(tss, gene), True)
def test_has_antisense_association_10(self):
"""None - out of range"""
tss = TSS("genomeX", 201, "-")
gene = Gene("genomeX", "g", "g", 10, 100, "+")
self.assertEqual(
self.tss_gene_mapper._has_antisense_association(tss, gene), None)
def test_has_antisense_association_8(self):
"""True - antisense"""
tss = TSS("genomeX", 200, "-")
gene = Gene("genomeX", "g", "g", 10, 100, "+")
self.assertEqual(
self.tss_gene_mapper._has_antisense_association(tss, gene), True)
def test_has_antisense_association_7(self):
"""True - antisense and inside the range"""
tss = TSS("genomeX", 900, "-")
gene = Gene("genomeX", "g", "g", 1000, 1100, "+")
self.assertEqual(
self.tss_gene_mapper._has_antisense_association(tss, gene), True)
def test_has_5_prime_association_10(self):
"""None - in 3' region"""
tss = TSS("genomeX", 5, "-")
gene = Gene("genomeX", "g", "g", 10, 100, "-")
self.assertEqual(
self.tss_gene_mapper._has_5_prime_association(tss, gene), None)
def test_has_internal_association_8(self):
"""None - on the first base => 5' leaderless """
tss = TSS("genomeX", 100, "-")
gene = Gene("genomeX", "g", "g", 10, 100, "-")
self.assertEqual(
self.tss_gene_mapper._has_internal_association(tss, gene), None)
def test_init_with_extra(self):
tss = TSS("plasmidY", "30", "+", extra="weak")
self.assertEqual(tss.seq_id, "plasmidY")
self.assertEqual(tss.pos, 30)
self.assertEqual(tss.strand, "+")
self.assertEqual(tss.extra, "weak")