def test_closest_by_feature_multiple_beds(self):
"""
Tests multiple features and multiple beds
"""
#makes bedtool to test -
bedtool = pybedtools.BedTool("""chr1 299 300 bar 0 -
chr1 301 400 bar 0 -
chr1 89 200 foo 0 +
chr1 91 200 foo 0 +""",
from_string=True)
closest_feature = pybedtools.BedTool("""chr1 310 400 bar 0 -\n
chr1 300 350 bar 0 -\n
chr1 111 200 foo 0 +\n
chr1 90 150 foo 0 +\n""",
from_string=True)
result = closest_by_feature(bedtool, closest_feature)
self.assertEqual(
str(
pybedtools.BedTool(
"""chr1 299 300 bar 0 - chr1 300 350 bar 0 - 1\n
chr1 301 400 bar 0 - chr1 300 350 bar 0 - -1\n
chr1 89 200 foo 0 + chr1 90 150 foo 0 + -1\n
chr1 91 200 foo 0 + chr1 90 150 foo 0 + 1\n""",
from_string=True)), str(result))
def test_closest_by_feature_multiple_beds(self):
"""
Tests multiple features and multiple beds
"""
#makes bedtool to test -
bedtool = pybedtools.BedTool("""chr1 299 300 bar 0 -
chr1 301 400 bar 0 -
chr1 89 200 foo 0 +
chr1 91 200 foo 0 +""", from_string=True)
closest_feature = pybedtools.BedTool("""chr1 310 400 bar 0 -\n
chr1 300 350 bar 0 -\n
chr1 111 200 foo 0 +\n
chr1 90 150 foo 0 +\n""", from_string=True)
result = closest_by_feature(bedtool, closest_feature)
self.assertEqual(str(pybedtools.BedTool("""chr1 299 300 bar 0 - chr1 300 350 bar 0 - 1\n
chr1 301 400 bar 0 - chr1 300 350 bar 0 - -1\n
chr1 89 200 foo 0 + chr1 90 150 foo 0 + -1\n
chr1 91 200 foo 0 + chr1 90 150 foo 0 + 1\n""", from_string=True)), str(result))
def test_closest_by_feature_negative_strand(self):
"""
Tests negative strand on closets_by_feature
"""
#makes bedtool to test -
bedtool = pybedtools.BedTool("chr1 100 200 foo 0 -", from_string=True)
closest_feature = pybedtools.BedTool("""chr1 111 200 foo 0 -\n
chr1 90 150 foo 0 -""", from_string=True)
result = closest_by_feature(bedtool, closest_feature)
self.assertEqual("\t".join("chr1 100 200 foo 0 - chr1 90 150 foo 0 - -10".split()) + "\n", str(result))
def test_closest_by_feature_negative_strand(self):
"""
Tests negative strand on closets_by_feature
"""
#makes bedtool to test -
bedtool = pybedtools.BedTool("chr1 100 200 foo 0 -", from_string=True)
closest_feature = pybedtools.BedTool("""chr1 111 200 foo 0 -\n
chr1 90 150 foo 0 -""",
from_string=True)
result = closest_by_feature(bedtool, closest_feature)
self.assertEqual(
"\t".join("chr1 100 200 foo 0 - chr1 90 150 foo 0 - -10".split())
+ "\n", str(result))
def test_closest_by_feature_positive_strand(self):
"""
Tests custom closest feature function, need 4 tests, + on tool - on
features and all other combinations
"""
#makes bedtool to test +
bedtool = pybedtools.BedTool("chr1 100 200 foo 0 +", from_string=True)
closest_feature = pybedtools.BedTool("""chr1 111 200 foo 0 +\n
chr1 90 150 foo 0 +""", from_string=True)
result = closest_by_feature(bedtool, closest_feature)
self.assertEqual("\t".join("chr1 100 200 foo 0 + chr1 90 150 foo 0 + 10".split()) + "\n", str(result))
def test_closest_by_feature_positive_strand(self):
"""
Tests custom closest feature function, need 4 tests, + on tool - on
features and all other combinations
"""
#makes bedtool to test +
bedtool = pybedtools.BedTool("chr1 100 200 foo 0 +", from_string=True)
closest_feature = pybedtools.BedTool("""chr1 111 200 foo 0 +\n
chr1 90 150 foo 0 +""",
from_string=True)
result = closest_by_feature(bedtool, closest_feature)
self.assertEqual(
"\t".join("chr1 100 200 foo 0 + chr1 90 150 foo 0 + 10".split()) +
"\n", str(result))