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import pybedtools
import six
import sys
import os, difflib
from .tfuncs import setup_module, teardown_module, testdir, test_tempdir, unwriteable
import pytest
def fix(x):
"""
Replaces spaces with tabs, removes spurious newlines, and lstrip()s each
line. Makes it really easy to create BED files on the fly for testing and
checking.
"""
s = ""
for i in x.splitlines():
i = i.strip()
if len(i) == 0:
continue
i = i.split()
i = '\t'.join(i)+'\n'
s += i
return s
def test_isBAM():
bam = pybedtools.example_filename('x.bam')
notabam = pybedtools.example_filename('a.bed')
open('tiny.txt', 'w').close()
assert pybedtools.helpers.isBAM(bam)
assert not pybedtools.helpers.isBAM(notabam)
assert not pybedtools.helpers.isBAM('tiny.txt')
os.unlink('tiny.txt')
def test_cleanup():
"""
make sure the tempdir and cleanup work
"""
#assert os.path.abspath(pybedtools.get_tempdir()) == os.path.abspath('.')
# make a fake tempfile, not created during this pybedtools session
pybedtools.cleanup()
testfn = os.path.join(test_tempdir, 'pybedtools.TESTING.tmp')
os.system('touch %s' % testfn)
assert os.path.exists(testfn)
# make some temp files
a = pybedtools.BedTool(os.path.join(testdir, 'data', 'a.bed'))
b = pybedtools.BedTool(os.path.join(testdir, 'data', 'b.bed'))
c = a.intersect(b)
# after standard cleanup, c's fn should be gone but the fake one still
# there...
pybedtools.cleanup(verbose=True)
assert os.path.exists(testfn)
assert not os.path.exists(c.fn)
# Unless we force the removal of all temp files.
pybedtools.cleanup(remove_all=True)
assert not os.path.exists(testfn)
# a.fn and b.fn better be there still!
assert os.path.exists(a.fn)
assert os.path.exists(b.fn)
# Test disabled, since we are no longer checking for pre-v2.15 versions by using
# separate program calls
#
# TODO: remove this once v2.15 support is fully deprecated.
#
# def test_bedtools_check():
# # this should run fine (especially since we've already imported pybedtools)
# pybedtools.check_for_bedtools()
#
# assert_raises(OSError, pybedtools.check_for_bedtools, **dict(program_to_check='nonexistent', force_check=True))
def test_call():
tmp = os.path.join(pybedtools.get_tempdir(), 'test.output')
from pybedtools.helpers import call_bedtools, BEDToolsError
with pytest.raises(BEDToolsError):
call_bedtools(*(['intersectBe'], tmp))
a = pybedtools.example_bedtool('a.bed')
# momentarily redirect stderr to file so the error message doesn't spew all
# over the place when testing
orig_stderr = sys.stderr
sys.stderr = open(a._tmp(), 'w')
sys.stderr = orig_stderr
pybedtools.set_bedtools_path('nonexistent')
a = pybedtools.example_bedtool('a.bed')
with pytest.raises(NotImplementedError):
a.intersect(a)
pybedtools.set_bedtools_path()
a = pybedtools.example_bedtool('a.bed')
assert a.intersect(a,u=True) == a
def test_chromsizes():
with pytest.raises(OSError):
pybedtools.get_chromsizes_from_ucsc('dm3', mysql='wrong path', fetchchromsizes='wrongtoo')
with pytest.raises(ValueError):
pybedtools.get_chromsizes_from_ucsc('dm3', timeout=0)
try:
print(pybedtools.chromsizes('dm3'))
print(pybedtools.get_chromsizes_from_ucsc('dm3'))
assert pybedtools.chromsizes('dm3') == pybedtools.get_chromsizes_from_ucsc('dm3')
hg17 = pybedtools.chromsizes('hg17')
assert hg17['chr1'] == (0, 245522847)
fn = pybedtools.chromsizes_to_file(hg17, fn='hg17.genome')
expected = 'chr1\t245522847\n'
results = open(fn).readline()
print(results)
assert expected == results
# make sure the tempfile version works, too
fn = pybedtools.chromsizes_to_file(hg17, fn=None)
expected = 'chr1\t245522847\n'
results = open(fn).readline()
print(results)
assert expected == results
with pytest.raises(OSError):
pybedtools.get_chromsizes_from_ucsc(
**dict(genome='hg17', mysql='nonexistent', fetchchromsizes='missing'))
os.unlink('hg17.genome')
except OSError:
sys.stdout.write("mysql error -- test for chromsizes from UCSC didn't run")
def test_ff_center():
from pybedtools.featurefuncs import center
a = pybedtools.example_bedtool('a.bed')
b = a.each(center, width=10)
expected = fix("""
chr1 45 55 feature1 0 +
chr1 145 155 feature2 0 +
chr1 320 330 feature3 0 -
chr1 920 930 feature4 0 +""")
assert str(b) == expected
def test_getting_example_beds():
assert 'a.bed' in pybedtools.list_example_files()
a_fn = pybedtools.example_filename('a.bed')
assert a_fn == os.path.join(testdir, 'data', 'a.bed')
a = pybedtools.example_bedtool('a.bed')
assert a.fn == os.path.join(testdir, 'data', 'a.bed')
# complain appropriately if nonexistent paths are asked for
e = FileNotFoundError if six.PY3 else ValueError
with pytest.raises(e):
pybedtools.example_filename('nonexistent')
with pytest.raises(e):
pybedtools.example_bedtool('nonexistent')
with pytest.raises(e):
pybedtools.set_tempdir('nonexistent')
def teardown():
# always run this!
pybedtools.cleanup(remove_all=True)
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