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from fastinterval import Interval, Genome, MinimalSpanningSet
import fastinterval
import pyfasta
import doctest
suite = doctest.DocTestSuite(fastinterval)
def test_Interval_from_string():
a = Interval.from_string('chr1:10858-10967:1')
assert a.chrom == 'chr1'
assert a.start == 10858
assert a.end == 10967
assert a.strand == 1
a = Interval.from_string('chr1:10858-10967:-1')
assert a.chrom == 'chr1'
assert a.start == 10858
assert a.end == 10967
assert a.strand == -1
def test_Interval_sequence():
genome = pyfasta.Fasta('test/example.fa')
l1 = Interval.from_string('1:858-967:1', genome=genome)
l2 = Interval.from_string('1:858-967:-1', genome=genome)
print l1.sequence
print l2.sequence
assert l1.sequence != l2.sequence
def test_Genome():
genome = Genome('test/example.fa')
i1 = genome.interval(10, 20, chrom='1')
print 'genome is', i1.genome
assert i1.genome == genome.fasta
assert i1.sequence
def test_Interval_distance():
l1 = Interval.from_string('chr1:10858-10967:1')
l2 = Interval.from_string('chr1:10858-10967:-1')
assert l1.distance(l2) == 0
l3 = Interval.from_string('chr1:10968-10977:-')
print l1.distance(l3)
assert l1.distance(l3) == 1
assert l3.distance(l1) == 1
def test_Interval_span():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:20858-30000:-1')
l3 = Interval.from_string('chr2:20858-30000:-1')
ex = l1.span(l2)
print ex
assert ex.start == 10000
assert ex.end == 30000
ex = l2.span(l1)
assert ex.start == 10000
assert ex.end == 30000
try:
l1.span(l3)
assert False
except:
pass
def test_Interval_overlaps():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-21000:-1')
l3 = Interval.from_string('chr1:20858-30000:-1')
l4 = Interval.from_string('chr1:30000-30001:-1')
assert l1.overlaps(l2)
assert l2.overlaps(l3)
assert not l1.overlaps(l3)
assert not l3.overlaps(l4)
def test_Interval_is_contiguous():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-21000:-1')
l3 = Interval.from_string('chr1:20858-30000:-1')
l4 = Interval.from_string('chr1:30000-30001:-1')
print l1.distance(l2) == 0
assert l1.is_contiguous(l2)
assert l2.is_contiguous(l3)
assert not l1.is_contiguous(l3)
assert l3.is_contiguous(l4)
def test_Interval_contains():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-10964:-1')
l3 = Interval.from_string('chr1:20858-30001:-1')
l4 = Interval.from_string('chr1:30000-30003:-1')
assert l2 in l1
assert not l1 in l2
assert not l3 in l4
def test_Interval_intersection():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-10964:-1')
i = l1.intersection(l2)
assert i.start == l2.start
assert i.end == l2.end
assert i.chrom == l2.chrom
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-11000:-1')
i = l1.intersection(l2)
assert i.start == l2.start
assert i.end == l1.end
assert i.chrom == l2.chrom
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr2:10858-10964:-1')
i = l1.intersection(l2)
assert i is None
def test_Interval_union():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-10964:-1')
i = l1.union(l2)
assert i.start == l1.start
assert i.end == l1.end
assert i.chrom == l2.chrom
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-11000:-1')
i = l1.union(l2)
assert i.start == l1.start
assert i.end == l2.end
assert i.chrom == l2.chrom
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr2:10858-10964:-1')
i = l1.intersection(l2)
assert i is None
def test_Interval_sub():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-10964:-1')
l3 = Interval.from_string('chr2:10858-10964:-1')
i = l1 - l2
print i
assert len(i)==2
l = i[0]
r = i[1]
assert l.start == 10000
assert l.end == 10858
assert r.start == 10964
assert r.end == 10967
assert len(l1 - l3) == 1
def test_Interval_merge():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-12964:-1')
l3 = Interval.from_string('chr1:10858-10964:-1')
merged = Interval.merge([l1,l2,l3])
assert len(merged) == 1
m = merged[0]
assert m.start == 10000
assert m.end == 12964
def test_find_minimal_spanning_set():
targets = [
Interval.from_string('chr1:10000-11000:+'),
Interval.from_string('chr1:12000-13000:+')
]
candidates = [
Interval.from_string('chr1:10000-10500:+'),
Interval.from_string('chr1:10100-10600:+'),
Interval.from_string('chr1:10300-11700:+'),
Interval.from_string('chr1:10500-11000:+'),
Interval.from_string('chr1:10700-11100:+'),
]
reads = MinimalSpanningSet(targets, candidates)
n_reads = len(reads.chosen)
print 'chose', reads.chosen
print 'n_reads', n_reads
assert n_reads == 2
targets = [
Interval.from_string('chr1:12000-13000:+')
]
candidates = [
Interval.from_string('chr1:10000-10500:+'),
Interval.from_string('chr1:10100-10600:+'),
Interval.from_string('chr1:10300-11700:+'),
Interval.from_string('chr1:10500-11000:+'),
Interval.from_string('chr1:10700-11100:+'),
]
# this example is constructed into fooling the greedy algorithm
# to choose one too many
reads = MinimalSpanningSet(targets, candidates)
assert len(reads.chosen) == 0
targets = [
Interval.from_string('chr1:12000-13000:+')
]
candidates = [
Interval.from_string('chr1:12000-12500:+'),
Interval.from_string('chr1:12500-13000:+'),
Interval.from_string('chr1:12100-12900:+'),
]
reads = MinimalSpanningSet(targets, candidates)
assert len(reads.chosen) == 2
def test_add_border():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = l1.add_border(upstream=50, downstream=100)
assert l2.start == 10000 - 50
assert l2.end == 10967 + 100
def test_truncate():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = l1.truncate(100)
assert l2.start == 10000
assert l2.end == 10100
l1 = Interval.from_string('chr1:10000-10967:-1')
l2 = l1.truncate(100)
assert l2.start == 10867
assert l2.end == 10967
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