def test___neq(self, location_with_region_name, location):
from outrigger.region import Region
r1 = Region(location_with_region_name)
r2 = Region(location)
assert r1.__neq__(r2)
def test___eq(self, location_with_region_name):
from outrigger.region import Region
r1 = Region(location_with_region_name)
r2 = Region(location_with_region_name)
assert r1 == r2
def test___neq(self, location_with_region_name, location):
from outrigger.region import Region
r1 = Region(location_with_region_name)
r2 = Region(location)
assert r1.__neq__(r2)
def test_overlaps_false_different_chrom(self, location):
from outrigger.region import Region
r1 = Region(location)
r2 = Region('chr2:400-500:-')
assert not r1.overlaps(r2)
assert not r2.overlaps(r1)
def test_overlaps_true(self, location_with_region_name, location):
from outrigger.region import Region
r1 = Region(location_with_region_name)
r2 = Region(location)
assert r1.overlaps(r2)
assert r2.overlaps(r1)
def test___str_with_region_name(self, location_with_region_name):
from outrigger.region import Region
r = Region(location_with_region_name)
true = 'outrigger.Region ({0})'.format(location_with_region_name)
assert str(r) == true
def test___str(self, location):
from outrigger.region import Region
r = Region(location)
true = 'outrigger.Region ({0})'.format(location)
assert str(r) == true
def test__stop(self, location):
from outrigger.region import Region
r = Region(location)
true__stop = -r.stop if r.strand == '-' else r.stop
assert r._stop == true__stop
def test___init_region_name(self, location_with_region_name):
from outrigger.region import Region
r = Region(location_with_region_name)
assert r.region == 'junction'
assert r.chrom == 'chr1'
assert r.start == 100
assert r.stop == 200
assert r.strand == '+'
assert r.name == location_with_region_name
def _get_junction23(row):
"""Make incompatible junction between exons2 and 3 for MXE
Parameters
----------
row : pandas.Series
A row containing "junction13" and "junction24" names in the index,
which contain outrigger.Region values
"""
junction13 = row['junction13']
junction24 = row['junction24']
if junction13.strand == "+":
return Region(region='junction', chrom=junction13.chrom,
start=junction24.start, stop=junction13.stop,
strand=junction13.strand)
if junction13.strand == "-":
return Region(region='junction', chrom=junction13.chrom,
start=junction13.start, stop=junction24.stop,
strand=junction13.strand)
def test___init(self, location):
from outrigger.region import Region
r = Region(location)
assert r.region is None
assert r.chrom == 'chr1'
assert r.start == 100
assert r.stop == 200
assert r.strand == location[-1]
assert r.name == location
def test_overlaps_false_different_chrom(self, location):
from outrigger.region import Region
r1 = Region(location)
r2 = Region('chr2:400-500:-')
assert not r1.overlaps(r2)
assert not r2.overlaps(r1)
def test_overlaps_true(self, location_with_region_name, location):
from outrigger.region import Region
r1 = Region(location_with_region_name)
r2 = Region(location)
assert r1.overlaps(r2)
assert r2.overlaps(r1)
def test___eq_not_region(self, location_with_region_name):
from outrigger.region import Region
r1 = Region(location_with_region_name)
assert not r1 == location_with_region_name
def test___len(self, location):
from outrigger.region import Region
r = Region(location)
assert len(r) == 101
def test___init_start_larger_than_stop(self):
from outrigger.region import Region
Region('chr1:200-100:+')
