def test_genes_within_iterable(testRefGen):
random_gene = testRefGen.random_gene()
bigger_locus = Locus(random_gene.chrom,
start=random_gene.start - 100,
end=random_gene.end + 100)
genes = testRefGen.genes_within([bigger_locus, bigger_locus], chain=True)
assert random_gene in genes
def test_genes_within(testRefGen):
random_gene = testRefGen.random_gene()
bigger_locus = Locus(random_gene.chrom,
start=random_gene.start - 100,
end=random_gene.end + 100)
genes = testRefGen.genes_within(bigger_locus)
assert random_gene in genes
def testTerm():
loci = [
# Overlapping Loci, No windows
Locus(1, 100, 500, score=0),
Locus(1, 400, 700, score=5),
# Loci with Overlapping windows
Locus(2, 100, 200, window=100, score=0),
Locus(2, 300, 500, window=100, score=5),
# SNPs with overlapping windows
Locus(3, 100, window=50, score=5),
Locus(3, 200, window=50, score=0),
# Three overlapping loci, one not
Locus(4, 100, window=80, score=1),
Locus(4, 200, window=80, score=2),
Locus(4, 300, window=80, score=3),
Locus(4, 400, window=10, score=4) # <- one not
]
return Term('test', desc='hello', loci=loci, attr1=True, attr2=False)
def test_flank_limit_for_candidate_genes_from_SNP(testRefGen):
random_gene = testRefGen.random_gene()
downstream = testRefGen.downstream_genes(
random_gene,gene_limit=10,window_size=50e6
)
test_snp = Locus(downstream[5].chrom,downstream[5].start,window=50e6)
# Create a Locus that is on gene 5
candidates = testRefGen.candidate_genes(
test_snp,flank_limit=5,window_size=50e6
)
assert len(candidates) == 11
def test_candidate_genes_from_SNP(testRefGen):
random_gene = testRefGen.random_gene()
# grab a bunch of downstream genes
down1,down2 = testRefGen.downstream_genes(
random_gene,gene_limit=2,window_size=50e6
)
# Create a Locus that is on gene 5
test_snp = Locus(
down1.chrom,
down1.start-50,
end=down2.end+50,
window=50e6
)
candidates = testRefGen.candidate_genes(
test_snp,flank_limit=5,chain=False
)
assert len(candidates) == 12
def test_candidate_genes_from_SNP(testRefGen):
random_gene = testRefGen.random_gene()
# grab a bunch of downstream genes
down1,down2 = testRefGen.downstream_genes(
random_gene,gene_limit=2,window_size=50e6
)
# Create a Locus that is on gene 5
test_snp = Locus(
down1.chrom,
down1.start-50,
end=down2.end+50,
window=50e6
)
candidates = testRefGen.candidate_genes(
test_snp,flank_limit=5,chain=False,
include_rank_intervening=True,
include_parent_locus=True,
include_parent_attrs='all',
include_num_intervening=True,
include_num_siblings=True,
include_SNP_distance=True
)
assert len(candidates) == 12
def test_add_Locus(testTerm):
new_locus = Locus(6, 100)
testTerm.add_locus(new_locus)
assert new_locus in testTerm.loci
testTerm.loci.remove(new_locus)
def test_flanking_genes_includes_within_genes_for_SNPS(testRefGen):
random_gene = testRefGen.random_gene()
# test snp
test_snp = Locus(random_gene.chrom,random_gene.start,window=50e5)
flanking = testRefGen.flanking_genes(test_snp)
assert random_gene not in flanking
def test_bootstrap_candidate_length_equal_from_SNP(testRefGen):
random_gene = testRefGen.random_gene()
test_snp = Locus(random_gene.chrom,random_gene.start,window=50e6)
candidates = testRefGen.candidate_genes(test_snp)
bootstraps = testRefGen.bootstrap_candidate_genes(test_snp)
assert len(candidates) == len(bootstraps)
def LocusX():
return Locus(1, 100, 200)
def test_encompassing_genes(testRefGen):
rg = testRefGen.random_gene()
middle = int((rg.start+rg.end)/2)
assert rg in testRefGen.encompassing_genes(Locus(rg.chrom,middle))
def LocusY():
return Locus(1, 300, 400)
def test_flanking_loci(testTerm):
assert len(testTerm.flanking_loci(Locus(4, 250), window_size=100)) == 2
assert len(testTerm.flanking_loci(Locus(4, 250), window_size=400)) == 4
def test_distance_between_loci():
x = Locus(1, 100, 200)
y = Locus(1, 300, 400)
assert x - y == 99
def test_init():
x = Term('testTerm',
desc='for testing',
loci=[Locus(1, 2), Locus(1, 3)],
foo='bar')
def test_init():
x = Term("testTerm",
desc="for testing",
loci=[Locus(1, 2), Locus(1, 3)],
foo="bar")
def simple_Locus():
return Locus(1, 100, 200)