def test_intron_exon_reads():
gff = pybedtools.example_filename('gdc.gff')
bam = pybedtools.example_filename('gdc.bam')
cmds = [
'intron_exon_reads.py',
'--gff', gff, '--bam', bam, '--processes', '2']
out = sp.check_output(cmds, universal_newlines=True)
assert out == dedent(
"""\
exon_only 3
intron_only 3
intron_and_exon 1
""")
cmds = [
'intron_exon_reads.py',
'--gff', gff, '--bam', bam, '--processes', '2', '--stranded']
out = sp.check_output(cmds, universal_newlines=True)
assert out == dedent(
"""\
exon_only 0
intron_only 0
intron_and_exon 0
""")
def test_intron_exon_reads():
gff = pybedtools.example_filename("gdc.gff")
bam = pybedtools.example_filename("gdc.bam")
cmds = [
"intron_exon_reads.py", "--gff", gff, "--bam", bam, "--processes", "2"
]
out = sp.check_output(cmds, universal_newlines=True)
assert out == dedent("""\
exon_only 3
intron_only 3
intron_and_exon 1
""")
cmds = [
"intron_exon_reads.py",
"--gff",
gff,
"--bam",
bam,
"--processes",
"2",
"--stranded",
]
out = sp.check_output(cmds, universal_newlines=True)
assert out == dedent("""\
exon_only 0
intron_only 0
intron_and_exon 0
""")
def test_bed_methods():
"""
Generator that yields tests, inserting different versions of `bed` as needed
"""
for method, send_kwargs, expected in parse_yaml(config_fn):
ignore = ['a', 'b','abam','i']
skip_test = False
for i in ignore:
if i in send_kwargs:
skip_test = True
if skip_test:
continue
if 'bed' not in send_kwargs:
continue
if 'files' in send_kwargs:
send_kwargs['files'] = [pybedtools.example_filename(i) for i in send_kwargs['files']]
if 'bams' in send_kwargs:
send_kwargs['bams'] = [pybedtools.example_filename(i) for i in send_kwargs['bams']]
if 'fi' in send_kwargs:
send_kwargs['fi'] = pybedtools.example_filename(send_kwargs['fi'])
orig_bed = pybedtools.example_bedtool(send_kwargs['bed'])
del send_kwargs['bed']
done = []
for kind_bed in ('filename', 'generator', 'stream', 'gzip'):
bed = converter[kind_bed](orig_bed)
kind = 'i=%(kind_bed)s' % locals()
f = partial(run, method, bed, expected, **send_kwargs)
f.description = '%(method)s, %(kind)s, %(send_kwargs)s' % locals()
yield (f, )
def main():
ap = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
ap.add_argument('--bed', help='BED file of e.g. peaks')
ap.add_argument('--gff', help='GFF file of e.g. annotations')
ap.add_argument('--out', default='out.png', help='Output PNG file')
ap.add_argument('--stranded', action='store_true',
help='Use strand-specific intersections')
ap.add_argument('--include', nargs='*', help='Featuretypes to include')
ap.add_argument('--exclude', nargs='*', help='Featuretypes to exclude')
ap.add_argument('--thresh', type=float, help='Threshold percentage below which output will be suppressed')
ap.add_argument('--test', action='store_true',
help='Run test, overwriting all other args')
args = ap.parse_args()
if not args.test:
if args.include and args.exclude:
raise ValueError('Cannot specify both --include and --exclude')
make_pie(bed=args.bed,
gff=args.gff,
out=args.out,
thresh=args.thresh,
stranded=args.stranded,
include=args.include,
exclude=args.exclude)
else:
make_pie(bed=pybedtools.example_filename('gdc.bed'),
gff=pybedtools.example_filename('gdc.gff'),
stranded=True,
out='out.png',
include=['CDS',
'intron',
'five_prime_UTR',
'three_prime_UTR'])
def test_intron_exon_reads():
gff = pybedtools.example_filename('gdc.gff')
bam = pybedtools.example_filename('gdc.bam')
cmds = [
'intron_exon_reads.py',
'--gff', gff, '--bam', bam, '--processes', '2']
out = sp.check_output(cmds, universal_newlines=True)
assert out == dedent(
"""\
exon_only 3
intron_only 3
intron_and_exon 1
""")
cmds = [
'intron_exon_reads.py',
'--gff', gff, '--bam', bam, '--processes', '2', '--stranded']
out = sp.check_output(cmds, universal_newlines=True)
assert out == dedent(
"""\
exon_only 0
intron_only 0
intron_and_exon 0
""")
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_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 main():
"""
Make a pie chart of features overlapping annotations (e.g., peaks in
introns, exons, etc)
"""
ap = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
ap.add_argument("--bed", help="BED file of e.g. peaks")
ap.add_argument("--gff", help="GFF file of e.g. annotations")
ap.add_argument("--out", default="out.png", help="Output PNG file")
ap.add_argument("--stranded",
action="store_true",
help="Use strand-specific intersections")
ap.add_argument("--include", nargs="*", help="Featuretypes to include")
ap.add_argument("--exclude", nargs="*", help="Featuretypes to exclude")
ap.add_argument(
"--thresh",
type=float,
help="Threshold percentage below which output will be "
"suppressed",
)
ap.add_argument(
"--test",
action="store_true",
help="Run test, overwriting all other args. Result will "
'be "out.png" in current directory.',
)
args = ap.parse_args()
if not (args.bed and args.gff) and not args.test:
ap.print_help()
sys.exit(1)
if not args.test:
if args.include and args.exclude:
raise ValueError("Cannot specify both --include and --exclude")
make_pie(
bed=args.bed,
gff=args.gff,
out=args.out,
thresh=args.thresh,
stranded=args.stranded,
include=args.include,
exclude=args.exclude,
)
else:
make_pie(
bed=pybedtools.example_filename("gdc.bed"),
gff=pybedtools.example_filename("gdc.gff"),
stranded=True,
out="out.png",
include=[
"exon", "CDS", "intron", "five_prime_UTR", "three_prime_UTR"
],
)
def test_issue_156():
# NOTE: this isn't appropriate for including in the test_iter cases, since
# that tests filenames, gzipped files, and iterators. There's no support
# for "list of iterators" as the `b` argument. Plus, here we're not
# concerned with the ability to handle those different input types -- just
# that lists of filenames works.
a = pybedtools.example_bedtool('a.bed')
b = [pybedtools.example_filename('b.bed'),
pybedtools.example_filename('c.gff')]
res = str(a.intersect(b))
assert res == fix(
"""
chr1 59 100 feature1 0 +
chr1 155 200 feature2 0 +
chr1 173 200 feature2 0 +
chr1 173 200 feature2 0 +
chr1 100 200 feature2 0 +
chr1 155 200 feature3 0 -
chr1 464 500 feature3 0 -
chr1 485 500 feature3 0 -
chr1 173 326 feature3 0 -
chr1 438 500 feature3 0 -
chr1 495 500 feature3 0 -
chr1 485 500 feature3 0 -
chr1 173 326 feature3 0 -
chr1 438 500 feature3 0 -
chr1 150 269 feature3 0 -
chr1 900 901 feature4 0 +
chr1 900 913 feature4 0 +
chr1 900 913 feature4 0 +
chr1 900 950 feature4 0 +
"""), res
res = str(a.intersect(b, wb=True, names=['B', 'C']))
assert res == fix(
"""
chr1 59 100 feature1 0 + C chr1 ucb gene 60 269 . - . ID=thaliana_1_6160_6269;match=fgenesh1_pg.C_scaffold_1000119;rname=thaliana_1_6160_6269
chr1 155 200 feature2 0 + B chr1 155 200 feature5 0 -
chr1 173 200 feature2 0 + C chr1 ucb CDS 174 326 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 173 200 feature2 0 + C chr1 ucb mRNA 174 326 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 100 200 feature2 0 + C chr1 ucb gene 60 269 . - . ID=thaliana_1_6160_6269;match=fgenesh1_pg.C_scaffold_1000119;rname=thaliana_1_6160_6269
chr1 155 200 feature3 0 - B chr1 155 200 feature5 0 -
chr1 464 500 feature3 0 - C chr1 ucb gene 465 805 . + . ID=thaliana_1_465_805;match=scaffold_801404.1;rname=thaliana_1_465_805
chr1 485 500 feature3 0 - C chr1 ucb CDS 486 605 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 173 326 feature3 0 - C chr1 ucb CDS 174 326 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 438 500 feature3 0 - C chr1 ucb CDS 439 630 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 495 500 feature3 0 - C chr1 ucb mRNA 496 576 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 485 500 feature3 0 - C chr1 ucb mRNA 486 605 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 173 326 feature3 0 - C chr1 ucb mRNA 174 326 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 438 500 feature3 0 - C chr1 ucb mRNA 439 899 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 150 269 feature3 0 - C chr1 ucb gene 60 269 . - . ID=thaliana_1_6160_6269;match=fgenesh1_pg.C_scaffold_1000119;rname=thaliana_1_6160_6269
chr1 900 901 feature4 0 + B chr1 800 901 feature6 0 +
chr1 900 913 feature4 0 + C chr1 ucb mRNA 631 913 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 900 913 feature4 0 + C chr1 ucb CDS 760 913 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 900 950 feature4 0 + C chr1 ucb CDS 706 1095 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
"""), res
def test_issue_156():
# NOTE: this isn't appropriate for including in the test_iter cases, since
# that tests filenames, gzipped files, and iterators. There's no support
# for "list of iterators" as the `b` argument. Plus, here we're not
# concerned with the ability to handle those different input types -- just
# that lists of filenames works.
a = pybedtools.example_bedtool("a.bed")
b = [
pybedtools.example_filename("b.bed"),
pybedtools.example_filename("c.gff")
]
res = str(a.intersect(b))
assert res == fix("""
chr1 59 100 feature1 0 +
chr1 155 200 feature2 0 +
chr1 173 200 feature2 0 +
chr1 173 200 feature2 0 +
chr1 100 200 feature2 0 +
chr1 155 200 feature3 0 -
chr1 464 500 feature3 0 -
chr1 485 500 feature3 0 -
chr1 173 326 feature3 0 -
chr1 438 500 feature3 0 -
chr1 495 500 feature3 0 -
chr1 485 500 feature3 0 -
chr1 173 326 feature3 0 -
chr1 438 500 feature3 0 -
chr1 150 269 feature3 0 -
chr1 900 901 feature4 0 +
chr1 900 913 feature4 0 +
chr1 900 913 feature4 0 +
chr1 900 950 feature4 0 +
"""), res
res = str(a.intersect(b, wb=True, names=["B", "C"]))
assert res == fix("""
chr1 59 100 feature1 0 + C chr1 ucb gene 60 269 . - . ID=thaliana_1_6160_6269;match=fgenesh1_pg.C_scaffold_1000119;rname=thaliana_1_6160_6269
chr1 155 200 feature2 0 + B chr1 155 200 feature5 0 -
chr1 173 200 feature2 0 + C chr1 ucb CDS 174 326 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 173 200 feature2 0 + C chr1 ucb mRNA 174 326 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 100 200 feature2 0 + C chr1 ucb gene 60 269 . - . ID=thaliana_1_6160_6269;match=fgenesh1_pg.C_scaffold_1000119;rname=thaliana_1_6160_6269
chr1 155 200 feature3 0 - B chr1 155 200 feature5 0 -
chr1 464 500 feature3 0 - C chr1 ucb gene 465 805 . + . ID=thaliana_1_465_805;match=scaffold_801404.1;rname=thaliana_1_465_805
chr1 485 500 feature3 0 - C chr1 ucb CDS 486 605 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 173 326 feature3 0 - C chr1 ucb CDS 174 326 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 438 500 feature3 0 - C chr1 ucb CDS 439 630 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 495 500 feature3 0 - C chr1 ucb mRNA 496 576 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 485 500 feature3 0 - C chr1 ucb mRNA 486 605 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 173 326 feature3 0 - C chr1 ucb mRNA 174 326 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 438 500 feature3 0 - C chr1 ucb mRNA 439 899 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 150 269 feature3 0 - C chr1 ucb gene 60 269 . - . ID=thaliana_1_6160_6269;match=fgenesh1_pg.C_scaffold_1000119;rname=thaliana_1_6160_6269
chr1 900 901 feature4 0 + B chr1 800 901 feature6 0 +
chr1 900 913 feature4 0 + C chr1 ucb mRNA 631 913 . + . ID=AT1G01010.mRNA;Parent=AT1G01010;rname=AT1G01010
chr1 900 913 feature4 0 + C chr1 ucb CDS 760 913 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
chr1 900 950 feature4 0 + C chr1 ucb CDS 706 1095 . + . Parent=AT1G01010.mRNA;rname=AT1G01010
"""), res
def test_gzipped_files_can_be_intersected():
agz = _make_temporary_gzip(pybedtools.example_filename('a.bed'))
bgz = _make_temporary_gzip(pybedtools.example_filename('b.bed'))
agz = pybedtools.BedTool(agz)
bgz = pybedtools.BedTool(bgz)
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
assert a.intersect(b) == agz.intersect(bgz) == a.intersect(bgz) == agz.intersect(b)
def test_links():
# have to be careful about the path, since it is embedded in the HTML
# output -- so make a copy of the example file, and delete when done.
os.system('cp %s a.links.bed' % pybedtools.example_filename('a.bed'))
a = pybedtools.BedTool('a.links.bed')
a = a.links()
exp = open(pybedtools.example_filename('a.links.html')).read()
obs = open(a.links_html).read()
print exp
print obs
assert exp == obs
os.unlink('a.links.bed')
def test_links():
# have to be careful about the path, since it is embedded in the HTML
# output -- so make a copy of the example file, and delete when done.
os.system('cp %s a.links.bed' % pybedtools.example_filename('a.bed'))
a = pybedtools.BedTool('a.links.bed')
a = a.links()
exp = open(pybedtools.example_filename('a.links.html')).read()
obs = open(a.links_html).read()
print exp
print obs
assert exp == obs
os.unlink('a.links.bed')
def test_gzip():
# make new gzipped files on the fly
agz = pybedtools.BedTool._tmp()
bgz = pybedtools.BedTool._tmp()
os.system('gzip -c %s > %s' % (pybedtools.example_filename('a.bed'), agz))
os.system('gzip -c %s > %s' % (pybedtools.example_filename('b.bed'), bgz))
agz = pybedtools.BedTool(agz)
bgz = pybedtools.BedTool(bgz)
assert agz.file_type == bgz.file_type == 'bed'
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
assert a.intersect(b) == agz.intersect(bgz) == a.intersect(bgz) == agz.intersect(b)
def test_gzip():
# make new gzipped files on the fly
agz = pybedtools.BedTool._tmp()
bgz = pybedtools.BedTool._tmp()
os.system("gzip -c %s > %s" % (pybedtools.example_filename("a.bed"), agz))
os.system("gzip -c %s > %s" % (pybedtools.example_filename("b.bed"), bgz))
agz = pybedtools.BedTool(agz)
bgz = pybedtools.BedTool(bgz)
assert agz.file_type == bgz.file_type == "bed"
a = pybedtools.example_bedtool("a.bed")
b = pybedtools.example_bedtool("b.bed")
assert a.intersect(b) == agz.intersect(bgz) == a.intersect(bgz) == agz.intersect(b)
def test_gzip():
# make new gzipped files on the fly
agz = pybedtools.BedTool._tmp()
bgz = pybedtools.BedTool._tmp()
os.system('gzip -c %s > %s' % (pybedtools.example_filename('a.bed'), agz))
os.system('gzip -c %s > %s' % (pybedtools.example_filename('b.bed'), bgz))
agz = pybedtools.BedTool(agz)
bgz = pybedtools.BedTool(bgz)
assert agz.file_type == bgz.file_type == 'bed'
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
assert a.intersect(b) == agz.intersect(bgz) == a.intersect(
bgz) == agz.intersect(b)
def test_issue_218():
from pybedtools.helpers import set_bedtools_path, get_bedtools_path
from pybedtools import BedTool
orig_path = get_bedtools_path()
# As pointed out in #222, example_bedtool behaves differently from BedTool.
# example_bedtool is defined in pybedtools.bedtool but pybedtools.BedTool
# is imported in pybedtools.__init__. So check various constructors here.
for constructor in (
lambda x: pybedtools.example_bedtool(x),
lambda x: pybedtools.BedTool(pybedtools.example_filename(x)),
lambda x: pybedtools.bedtool.BedTool(pybedtools.example_filename(x)),
# NOTE: we likely need recursive reloading (like IPython.deepreload)
# for this to work:
#
# lambda x: BedTool(pybedtools.example_filename(x)),
):
x = constructor('x.bed')
x.sort()
assert "Original BEDTools help" in pybedtools.bedtool.BedTool.sort.__doc__
assert "Original BEDTools help" in x.sort.__doc__
set_bedtools_path('nonexistent')
# Calling BEDTools with non-existent path, but the docstring should not
# have been changed.
with pytest.raises(OSError):
x.sort()
assert "Original BEDTools help" in x.sort.__doc__
# The class's docstring should have been reset though.
assert pybedtools.bedtool.BedTool.sort.__doc__ is None
# Creating a new BedTool object now that bedtools is not on the path
# should detect that, adding a method that raises
# NotImplementedError...
y = constructor('x.bed')
with pytest.raises(NotImplementedError):
y.sort()
# ...and correspondingly no docstring
assert y.sort.__doc__ is None
assert pybedtools.bedtool.BedTool.sort.__doc__ is None
# Reset the path, and ensure the resetting works
set_bedtools_path()
z = constructor('x.bed')
z.sort()
def test_issue_218():
from pybedtools.helpers import set_bedtools_path, get_bedtools_path
from pybedtools import BedTool
orig_path = get_bedtools_path()
# As pointed out in #222, example_bedtool behaves differently from BedTool.
# example_bedtool is defined in pybedtools.bedtool but pybedtools.BedTool
# is imported in pybedtools.__init__. So check various constructors here.
for constructor in (
lambda x: pybedtools.example_bedtool(x),
lambda x: pybedtools.BedTool(pybedtools.example_filename(x)),
lambda x: pybedtools.bedtool.BedTool(pybedtools.example_filename(x)
),
# NOTE: we likely need recursive reloading (like IPython.deepreload)
# for this to work:
#
# lambda x: BedTool(pybedtools.example_filename(x)),
):
x = constructor("x.bed")
x.sort()
assert "Original BEDTools help" in pybedtools.bedtool.BedTool.sort.__doc__
assert "Original BEDTools help" in x.sort.__doc__
set_bedtools_path("nonexistent")
# Calling BEDTools with non-existent path, but the docstring should not
# have been changed.
with pytest.raises(OSError):
x.sort()
assert "Original BEDTools help" in x.sort.__doc__
# The class's docstring should have been reset though.
assert pybedtools.bedtool.BedTool.sort.__doc__ is None
# Creating a new BedTool object now that bedtools is not on the path
# should detect that, adding a method that raises
# NotImplementedError...
y = constructor("x.bed")
with pytest.raises(NotImplementedError):
y.sort()
# ...and correspondingly no docstring
assert y.sort.__doc__ is None
assert pybedtools.bedtool.BedTool.sort.__doc__ is None
# Reset the path, and ensure the resetting works
set_bedtools_path()
z = constructor("x.bed")
z.sort()
def main():
"""
Make a pie chart of features overlapping annotations (e.g., peaks in
introns, exons, etc)
"""
ap = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
ap.add_argument('--bed', help='BED file of e.g. peaks')
ap.add_argument('--gff', help='GFF file of e.g. annotations')
ap.add_argument('--out', default='out.png', help='Output PNG file')
ap.add_argument('--stranded',
action='store_true',
help='Use strand-specific intersections')
ap.add_argument('--include', nargs='*', help='Featuretypes to include')
ap.add_argument('--exclude', nargs='*', help='Featuretypes to exclude')
ap.add_argument('--thresh',
type=float,
help='Threshold percentage below which output will be '
'suppressed')
ap.add_argument('--test',
action='store_true',
help='Run test, overwriting all other args. Result will '
'be "out.png" in current directory.')
args = ap.parse_args()
if not (args.bed and args.gff) and not args.test:
ap.print_help()
sys.exit(1)
if not args.test:
if args.include and args.exclude:
raise ValueError('Cannot specify both --include and --exclude')
make_pie(bed=args.bed,
gff=args.gff,
out=args.out,
thresh=args.thresh,
stranded=args.stranded,
include=args.include,
exclude=args.exclude)
else:
make_pie(bed=pybedtools.example_filename('gdc.bed'),
gff=pybedtools.example_filename('gdc.gff'),
stranded=True,
out='out.png',
include=[
'exon', 'CDS', 'intron', 'five_prime_UTR',
'three_prime_UTR'
])
def test_gzipped_files_are_iterable_as_normal():
agz = _make_temporary_gzip(pybedtools.example_filename('a.bed'))
agz = pybedtools.BedTool(agz)
a = pybedtools.example_bedtool('a.bed')
for i in agz:
print(i)
assert_list_equal(list(a), list(agz))
def test_cat():
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
b_fn = pybedtools.example_filename('b.bed')
assert a.cat(b) == a.cat(b_fn)
expected = fix("""
chr1 1 500
chr1 800 950
""")
assert a.cat(b) == expected
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
c = a.cat(b, postmerge=False)
assert len(a) + len(b) == len(c), (len(a), len(b), len(c))
print c
assert c == fix("""
chr1 1 100 feature1 0 +
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -
chr1 900 950 feature4 0 +
chr1 155 200 feature5 0 -
chr1 800 901 feature6 0 +
""")
def test_issue_178():
# Compatibility between py2/py3: py27 does not have FileNotFoundError, so
# set it to IOError (which does exist) for this function.
try:
FileNotFoundError
except NameError:
FileNotFoundError = IOError
try:
fn = pybedtools.example_filename('gdc.othersort.bam')
pybedtools.contrib.bigwig.bam_to_bigwig(fn, genome='dm3', output='tmp.bw')
x = pybedtools.contrib.bigwig.bigwig_to_bedgraph('tmp.bw')
assert x == fix(
'''
chr2L 70 75 1
chr2L 140 145 1
chr2L 150 155 1
chr2L 160 165 1
chr2L 210 215 1
chrX 10 15 1
chrX 70 75 1
chrX 140 145 1
''')
os.unlink('tmp.bw')
# If bedGraphToBigWig is not on the path, see
# https://github.com/daler/pybedtools/issues/227
except FileNotFoundError:
pass
def test_cat():
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
b_fn = pybedtools.example_filename('b.bed')
assert a.cat(b) == a.cat(b_fn)
expected = fix("""
chr1 1 500
chr1 800 950
""")
assert a.cat(b) == expected
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
c = a.cat(b, postmerge=False)
assert len(a) + len(b) == len(c), (len(a), len(b), len(c))
print c
assert c == fix("""
chr1 1 100 feature1 0 +
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -
chr1 900 950 feature4 0 +
chr1 155 200 feature5 0 -
chr1 800 901 feature6 0 +
""")
def test_gzipped_files_are_iterable_as_normal():
agz = _make_temporary_gzip(pybedtools.example_filename('a.bed'))
agz = pybedtools.BedTool(agz)
a = pybedtools.example_bedtool('a.bed')
for i in agz:
print(i)
assert list(a) == list(agz)
def test_issue_178():
# Compatibility between py2/py3: py27 does not have FileNotFoundError, so
# set it to IOError (which does exist) for this function.
try:
FileNotFoundError
except NameError:
FileNotFoundError = IOError
try:
fn = pybedtools.example_filename("gdc.othersort.bam")
pybedtools.contrib.bigwig.bam_to_bigwig(fn,
genome="dm3",
output="tmp.bw")
x = pybedtools.contrib.bigwig.bigwig_to_bedgraph("tmp.bw")
assert x == fix("""
chr2L 70 75 1
chr2L 140 145 1
chr2L 150 155 1
chr2L 160 165 1
chr2L 210 215 1
chrX 10 15 1
chrX 70 75 1
chrX 140 145 1
""")
os.unlink("tmp.bw")
# If bedGraphToBigWig is not on the path, see
# https://github.com/daler/pybedtools/issues/227
except FileNotFoundError:
pass
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 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 fetchSequence(chrName, start, end, fastq):
position = ' '.join([chrName, start, end])
#print(position)
bedpos = pybedtools.BedTool(position, from_string=True)
fasta = pybedtools.example_filename(fastq)
bedpos = bedpos.sequence(fi=fasta)
sequence = open(bedpos.seqfn).read()
return (sequence)
def _classifier():
c = Classifier(
bed=pybedtools.example_filename("gdc.bed"),
annotations=pybedtools.example_filename("gdc.gff"),
)
c.classify()
bed = pybedtools.example_bedtool("gdc.bed")
assert c.class_counts == {
frozenset(["UTR", "exon", "mRNA", "CDS", "tRNA", "gene"]): 1,
frozenset(["intron", "gene", "mRNA"]): 3,
frozenset([]): 1,
frozenset(["gene", "exon", "mRNA", "CDS"]): 2,
frozenset(["exon", "mRNA", "CDS", "tRNA", "intron", "gene"]): 1,
}
assert c.feature_classes == {
bed[0]: set(["."]),
bed[1]: set(["gene", "exon", "mRNA", "CDS"]),
bed[2]: set(["intron", "gene", "mRNA"]),
bed[3]: set(["intron", "gene", "mRNA"]),
bed[4]: set(["tRNA", "UTR", "exon", "mRNA", "CDS", "gene"]),
bed[5]: set(["gene", "exon", "mRNA", "CDS"]),
bed[6]: set(["intron", "gene", "mRNA"]),
bed[7]: set(["tRNA", "intron", "exon", "mRNA", "CDS", "gene"]),
}
print("use these indexes for debugging")
for i, f in enumerate(bed):
print(i, f)
for k, v in list(c.class_features.items()):
print(k)
for i in v:
print("\t" + str(i))
assert c.class_features == {
frozenset([]): [bed[0]],
frozenset(["intron", "gene", "mRNA"]): [bed[6], bed[2], bed[3]],
frozenset(["gene", "exon", "mRNA", "CDS"]): [bed[5], bed[1]],
frozenset(["UTR", "exon", "mRNA", "CDS", "tRNA", "gene"]): [bed[4]],
frozenset(["exon", "mRNA", "CDS", "tRNA", "intron", "gene"]): [bed[7]],
}
def main():
"""
Make a pie chart of features overlapping annotations (e.g., peaks in
introns, exons, etc)
"""
ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
ap.add_argument("--bed", help="BED file of e.g. peaks")
ap.add_argument("--gff", help="GFF file of e.g. annotations")
ap.add_argument("--out", default="out.png", help="Output PNG file")
ap.add_argument("--stranded", action="store_true", help="Use strand-specific intersections")
ap.add_argument("--include", nargs="*", help="Featuretypes to include")
ap.add_argument("--exclude", nargs="*", help="Featuretypes to exclude")
ap.add_argument("--thresh", type=float, help="Threshold percentage below which output will be " "suppressed")
ap.add_argument(
"--test",
action="store_true",
help="Run test, overwriting all other args. Result will " 'be "out.png" in current directory.',
)
args = ap.parse_args()
if not (args.bed and args.gff) and not args.test:
ap.print_help()
sys.exit(1)
if not args.test:
if args.include and args.exclude:
raise ValueError("Cannot specify both --include and --exclude")
make_pie(
bed=args.bed,
gff=args.gff,
out=args.out,
thresh=args.thresh,
stranded=args.stranded,
include=args.include,
exclude=args.exclude,
)
else:
make_pie(
bed=pybedtools.example_filename("gdc.bed"),
gff=pybedtools.example_filename("gdc.gff"),
stranded=True,
out="out.png",
include=["exon", "CDS", "intron", "five_prime_UTR", "three_prime_UTR"],
)
def test_links():
# have to be careful about the path, since it is embedded in the HTML
# output.
a = pybedtools.BedTool(
os.path.join(os.path.relpath(pybedtools.data_dir()), 'a.bed'))
a = a.links()
exp = open(pybedtools.example_filename('a.links.html')).read()
obs = open(a.links_html).read()
assert exp == obs
def get_sequence(reference_fasta, coordinates, strand):
"""Takes coordinates and returns sequence
bed_coor is space separated"""
bed_coor = pybedtools.BedTool(coordinates, from_string=True)
fasta = pybedtools.example_filename(reference_fasta)
seq = bed_coor.sequence(fi=fasta)
seq_str = open(seq.seqfn, 'r').read()
pybedtools.cleanup(remove_all=True)
return seq_str.replace('>', '').split('\n')[0:-1]
def _classifier():
c = Classifier(
bed=pybedtools.example_filename('gdc.bed'),
annotations=pybedtools.example_filename('gdc.gff'))
c.classify()
bed = pybedtools.example_bedtool('gdc.bed')
assert c.class_counts == {
frozenset(['UTR', 'exon', 'mRNA', 'CDS', 'tRNA', 'gene']): 1,
frozenset(['intron', 'gene', 'mRNA']): 3,
frozenset([]): 1,
frozenset(['gene', 'exon', 'mRNA', 'CDS']): 2,
frozenset(['exon', 'mRNA', 'CDS', 'tRNA', 'intron', 'gene']): 1}
assert c.feature_classes == {
bed[0]: set(['.']),
bed[1]: set(['gene', 'exon', 'mRNA', 'CDS']),
bed[2]: set(['intron', 'gene', 'mRNA']),
bed[3]: set(['intron', 'gene', 'mRNA']),
bed[4]: set(['tRNA', 'UTR', 'exon', 'mRNA', 'CDS', 'gene']),
bed[5]: set(['gene', 'exon', 'mRNA', 'CDS']),
bed[6]: set(['intron', 'gene', 'mRNA']),
bed[7]: set(['tRNA', 'intron', 'exon', 'mRNA', 'CDS', 'gene']),
}
print('use these indexes for debugging')
for i, f in enumerate(bed):
print(i, f)
for k, v in list(c.class_features.items()):
print(k)
for i in v:
print('\t' + str(i))
assert c.class_features == {
frozenset([]): [bed[0]],
frozenset(['intron', 'gene', 'mRNA']): [bed[6], bed[2], bed[3]],
frozenset(['gene', 'exon', 'mRNA', 'CDS']): [bed[5], bed[1]],
frozenset(['UTR', 'exon', 'mRNA', 'CDS', 'tRNA', 'gene']): [bed[4]],
frozenset(['exon', 'mRNA', 'CDS', 'tRNA', 'intron', 'gene']): [bed[7]],
}
def _get_sequence(chrom, pos, strand, genome):
a = pybedtools.BedTool("{0}\t{1}\t{2}\t.\t.\t{3}".format(chrom, pos-150, pos+150, strand), from_string=True)
fasta = pybedtools.example_filename(genome)
a = a.sequence(fi=fasta,s=True)
seq = open(a.seqfn).read().split("\n")
pre = seq[1][:150]
nt = seq[1][150]
post = seq[1][151:]
# print [pre, nt, post]
return [chrom , str(pos), "%s-%s-%s" % (pre, nt, post)]
def test_classifier():
c = Classifier(bed=pybedtools.example_filename('gdc.bed'),
annotations=pybedtools.example_filename('gdc.gff'))
c.classify()
bed = pybedtools.example_bedtool('gdc.bed')
assert c.class_counts == {
frozenset(['UTR', 'exon', 'mRNA', 'CDS', 'tRNA', 'gene']): 1,
frozenset(['intron', 'gene', 'mRNA']): 3,
frozenset([]): 1,
frozenset(['gene', 'exon', 'mRNA', 'CDS']): 2,
frozenset(['exon', 'mRNA', 'CDS', 'tRNA', 'intron', 'gene']): 1
}
assert c.feature_classes == {
bed[0]: set(['.']),
bed[1]: set(['gene', 'exon', 'mRNA', 'CDS']),
bed[2]: set(['intron', 'gene', 'mRNA']),
bed[3]: set(['intron', 'gene', 'mRNA']),
bed[4]: set(['tRNA', 'UTR', 'exon', 'mRNA', 'CDS', 'gene']),
bed[5]: set(['gene', 'exon', 'mRNA', 'CDS']),
bed[6]: set(['intron', 'gene', 'mRNA']),
bed[7]: set(['tRNA', 'intron', 'exon', 'mRNA', 'CDS', 'gene']),
}
print 'use these indexes for debugging'
for i, f in enumerate(bed):
print i, f
for k, v in c.class_features.items():
print k
for i in v:
print '\t' + str(i)
assert c.class_features == {
frozenset([]): [bed[0]],
frozenset(['intron', 'gene', 'mRNA']): [bed[6], bed[2], bed[3]],
frozenset(['gene', 'exon', 'mRNA', 'CDS']): [bed[5], bed[1]],
frozenset(['UTR', 'exon', 'mRNA', 'CDS', 'tRNA', 'gene']): [bed[4]],
frozenset(['exon', 'mRNA', 'CDS', 'tRNA', 'intron', 'gene']): [bed[7]],
}
def _classifier():
c = Classifier(bed=pybedtools.example_filename("gdc.bed"), annotations=pybedtools.example_filename("gdc.gff"))
c.classify()
bed = pybedtools.example_bedtool("gdc.bed")
assert c.class_counts == {
frozenset(["UTR", "exon", "mRNA", "CDS", "tRNA", "gene"]): 1,
frozenset(["intron", "gene", "mRNA"]): 3,
frozenset([]): 1,
frozenset(["gene", "exon", "mRNA", "CDS"]): 2,
frozenset(["exon", "mRNA", "CDS", "tRNA", "intron", "gene"]): 1,
}
assert c.feature_classes == {
bed[0]: set(["."]),
bed[1]: set(["gene", "exon", "mRNA", "CDS"]),
bed[2]: set(["intron", "gene", "mRNA"]),
bed[3]: set(["intron", "gene", "mRNA"]),
bed[4]: set(["tRNA", "UTR", "exon", "mRNA", "CDS", "gene"]),
bed[5]: set(["gene", "exon", "mRNA", "CDS"]),
bed[6]: set(["intron", "gene", "mRNA"]),
bed[7]: set(["tRNA", "intron", "exon", "mRNA", "CDS", "gene"]),
}
print "use these indexes for debugging"
for i, f in enumerate(bed):
print i, f
for k, v in c.class_features.items():
print k
for i in v:
print "\t" + str(i)
assert c.class_features == {
frozenset([]): [bed[0]],
frozenset(["intron", "gene", "mRNA"]): [bed[6], bed[2], bed[3]],
frozenset(["gene", "exon", "mRNA", "CDS"]): [bed[5], bed[1]],
frozenset(["UTR", "exon", "mRNA", "CDS", "tRNA", "gene"]): [bed[4]],
frozenset(["exon", "mRNA", "CDS", "tRNA", "intron", "gene"]): [bed[7]],
}
def test_links():
# have to be careful about the path, since it is embedded in the HTML
# output.
a = pybedtools.BedTool(
os.path.join(
os.path.relpath(pybedtools.data_dir()),
'a.bed'))
a = a.links()
exp = open(pybedtools.example_filename('a.links.html')).read()
obs = open(a.links_html).read()
assert exp == obs
def test_gzipped_output():
_filename = pybedtools.example_filename('a.bed')
compressed_file = pybedtools.BedTool(_filename).saveas(compressed=True)
# Open gzipped file in text mode
with gzip.open(compressed_file.fn, 'rt') as gf:
uncompressed_content = gf.read()
with open(_filename) as f:
original_content = f.read()
assert_equal(original_content, uncompressed_content)
def test_a_b_methods():
"""
Generator that yields tests, inserting different versions of `a` and `b` as
needed
"""
for method, send_kwargs, expected in parse_yaml(config_fn):
a_isbam = False
b_isbam = False
if 'abam' in send_kwargs:
send_kwargs['abam'] = pybedtools.example_filename(
send_kwargs['abam'])
send_kwargs['a'] = send_kwargs['abam']
a_isbam = True
if not (('a' in send_kwargs) and ('b' in send_kwargs)):
continue
# If abam, makes a BedTool out of it anyway.
orig_a = pybedtools.example_bedtool(send_kwargs['a'])
orig_b = pybedtools.example_bedtool(send_kwargs['b'])
del send_kwargs['a']
del send_kwargs['b']
if orig_a._isbam:
a_isbam = True
if orig_b._isbam:
b_isbam = True
for kind_a, kind_b in itertools.permutations(
('filename', 'generator', 'stream', 'gzip'), 2):
if a_isbam and (kind_a not in supported_bam):
continue
if b_isbam and (kind_b not in supported_bam):
continue
# Convert to file/generator/stream
bedtool = converter[kind_a](orig_a)
b = converter[kind_b](orig_b)
kind = 'a=%(kind_a)s, b=%(kind_b)s abam=%(a_isbam)s bbam=%(b_isbam)s' % locals(
)
send_kwargs['b'] = b
f = partial(run, method, bedtool, expected, **send_kwargs)
# Meaningful description
f.description = '%(method)s, %(kind)s, %(send_kwargs)s' % locals()
yield (f, )
def test_gzipped_output():
_filename = pybedtools.example_filename('a.bed')
compressed_file = pybedtools.BedTool(_filename).saveas(compressed=True)
# Open gzipped file in text mode
with gzip.open(compressed_file.fn, 'rt') as gf:
uncompressed_content = gf.read()
with open(_filename) as f:
original_content = f.read()
assert original_content == uncompressed_content
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
assert_raises(ValueError, pybedtools.example_filename, 'nonexistent')
assert_raises(ValueError, pybedtools.example_bedtool, 'nonexistent')
assert_raises(ValueError, pybedtools.set_tempdir, 'nonexistent')
def test_i_methods():
"""
Generator that yields tests, inserting different versions of `i` as needed
"""
for method, send_kwargs, expected in parse_yaml(config_fn):
i_isbam = False
if 'ibam' in send_kwargs:
i_isbam = True
send_kwargs['ibam'] = pybedtools.example_filename(
send_kwargs['ibam'])
send_kwargs['i'] = send_kwargs['ibam']
if ('a' in send_kwargs) and ('b' in send_kwargs):
continue
if ('i' not in send_kwargs) and ('ibam' not in send_kwargs):
continue
if 'files' in send_kwargs:
send_kwargs['files'] = [
pybedtools.example_filename(i) for i in send_kwargs['files']
]
orig_i = pybedtools.example_bedtool(send_kwargs['i'])
if orig_i._isbam:
i_isbam = True
del send_kwargs['i']
done = []
for kind_i in ('filename', 'generator', 'stream', 'gzip'):
if i_isbam:
if (kind_i not in supported_bam):
continue
i = converter[kind_i](orig_i)
kind = 'i=%(kind_i)s ibam=%(i_isbam)s' % locals()
f = partial(run, method, i, expected, **send_kwargs)
f.description = '%(method)s, %(kind)s, %(send_kwargs)s' % locals()
yield (f, )
def test_bed_methods():
"""
Generator that yields tests, inserting different versions of `bed` as needed
"""
for method, send_kwargs, expected in parse_yaml(config_fn):
ignore = ['a', 'b', 'abam', 'i']
skip_test = False
for i in ignore:
if i in send_kwargs:
skip_test = True
if skip_test:
continue
if 'bed' not in send_kwargs:
continue
if 'files' in send_kwargs:
send_kwargs['files'] = [
pybedtools.example_filename(i) for i in send_kwargs['files']
]
if 'bams' in send_kwargs:
send_kwargs['bams'] = [
pybedtools.example_filename(i) for i in send_kwargs['bams']
]
if 'fi' in send_kwargs:
send_kwargs['fi'] = pybedtools.example_filename(send_kwargs['fi'])
orig_bed = pybedtools.example_bedtool(send_kwargs['bed'])
del send_kwargs['bed']
done = []
for kind_bed in ('filename', 'generator', 'stream', 'gzip'):
bed = converter[kind_bed](orig_bed)
kind = 'i=%(kind_bed)s' % locals()
f = partial(run, method, bed, expected, **send_kwargs)
f.description = '%(method)s, %(kind)s, %(send_kwargs)s' % locals()
yield (f, )
def test_tabix():
a = pybedtools.example_bedtool('a.bed')
t = a.tabix()
assert t._tabixed()
results = str(t.tabix_intervals('chr1:99-200'))
print results
assert results == fix("""
chr1 1 100 feature1 0 +
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -""")
assert str(t.tabix_intervals(a[2])) == fix("""
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -""")
# clean up
fns = [
pybedtools.example_filename('a.bed.gz'),
pybedtools.example_filename('a.bed.gz.tbi'),
]
for fn in fns:
if os.path.exists(fn):
os.unlink(fn)
def test_tabix():
a = pybedtools.example_bedtool('a.bed')
t = a.tabix()
assert t._tabixed()
results = str(t.tabix_intervals('chr1:99-200'))
print results
assert results == fix("""
chr1 1 100 feature1 0 +
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -""")
assert str(t.tabix_intervals(a[2])) == fix("""
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -""")
# clean up
fns = [
pybedtools.example_filename('a.bed.gz'),
pybedtools.example_filename('a.bed.gz.tbi'),
]
for fn in fns:
if os.path.exists(fn):
os.unlink(fn)
def test_a_b_methods():
"""
Generator that yields tests, inserting different versions of `a` and `b` as
needed
"""
for method, send_kwargs, expected in parse_yaml(config_fn):
a_isbam = False
b_isbam = False
if 'abam' in send_kwargs:
send_kwargs['abam'] = pybedtools.example_filename(send_kwargs['abam'])
send_kwargs['a'] = send_kwargs['abam']
a_isbam = True
if not (('a' in send_kwargs) and ('b' in send_kwargs)):
continue
# If abam, makes a BedTool out of it anyway.
orig_a = pybedtools.example_bedtool(send_kwargs['a'])
orig_b = pybedtools.example_bedtool(send_kwargs['b'])
del send_kwargs['a']
del send_kwargs['b']
if orig_a._isbam:
a_isbam = True
if orig_b._isbam:
b_isbam = True
for kind_a, kind_b in itertools.permutations(('filename', 'generator', 'stream', 'gzip'), 2):
if a_isbam and (kind_a not in supported_bam):
continue
if b_isbam and (kind_b not in supported_bam):
continue
# Convert to file/generator/stream
bedtool = converter[kind_a](orig_a)
b = converter[kind_b](orig_b)
kind = 'a=%(kind_a)s, b=%(kind_b)s abam=%(a_isbam)s bbam=%(b_isbam)s' % locals()
send_kwargs['b'] = b
f = partial(run, method, bedtool, expected, **send_kwargs)
# Meaningful description
f.description = '%(method)s, %(kind)s, %(send_kwargs)s' % locals()
yield (f, )
def get_trinuc(bed_i, fa_loc):
"""Get trinucleotide context per DNV."""
trinuc_out_loc = 'trinuc_out/{}_trinuc.txt'.format(bed_i[:-4])
if os.path.exists(trinuc_out_loc):
return 'trinuc already made for ' + bed_i
dnv_bed = pybedtools.BedTool(bed_i)
# change start column to start-1, end to end+1
dnv_bed = dnv_bed.each(mod_start_end)
dnv_bed = dnv_bed.saveas()
# run getfasta using pybedtools wrapper
fasta = pybedtools.example_filename(fa_loc)
dnv_bed = dnv_bed.sequence(fi=fasta)
# save output sequence
write_trinuc(dnv_bed, trinuc_out_loc)
return bed_i + ' trinuc done'
def test_i_methods():
"""
Generator that yields tests, inserting different versions of `i` as needed
"""
for method, send_kwargs, expected in parse_yaml(config_fn):
i_isbam = False
if 'ibam' in send_kwargs:
i_isbam = True
send_kwargs['ibam'] = pybedtools.example_filename(send_kwargs['ibam'])
send_kwargs['i'] = send_kwargs['ibam']
if ('a' in send_kwargs) and ('b' in send_kwargs):
continue
if ('i' not in send_kwargs) and ('ibam' not in send_kwargs):
continue
if 'files' in send_kwargs:
send_kwargs['files'] = [pybedtools.example_filename(i) for i in send_kwargs['files']]
orig_i = pybedtools.example_bedtool(send_kwargs['i'])
if orig_i._isbam:
i_isbam = True
del send_kwargs['i']
done = []
for kind_i in ('filename', 'generator', 'stream', 'gzip'):
if i_isbam:
if (kind_i not in supported_bam):
continue
i = converter[kind_i](orig_i)
kind = 'i=%(kind_i)s ibam=%(i_isbam)s' % locals()
f = partial(run, method, i, expected, **send_kwargs)
f.description = '%(method)s, %(kind)s, %(send_kwargs)s' % locals()
yield (f, )
def test_cat():
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
b_fn = pybedtools.example_filename('b.bed')
assert a.cat(b) == a.cat(b_fn)
expected = fix("""
chr1 1 500
chr1 800 950
""")
assert a.cat(b) == expected
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
c = a.cat(b, postmerge=False)
assert len(a) + len(b) == len(c), (len(a), len(b), len(c))
def test_cat():
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
b_fn = pybedtools.example_filename('b.bed')
assert a.cat(b) == a.cat(b_fn)
expected = fix("""
chr1 1 500
chr1 800 950
""")
assert a.cat(b) == expected
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
c = a.cat(b, postmerge=False)
assert len(a) + len(b) == len(c), (len(a), len(b), len(c))
def test_gzipping_is_default_when_extension_is_dot_gz():
_filename = pybedtools.example_filename('a.bed')
with open(_filename) as f:
expected_content = f.read()
__, temp_filename = tempfile.mkstemp(suffix='.gz')
try:
bedtool = pybedtools.BedTool(_filename)
bedtool.saveas(fn=temp_filename)
with gzip.open(temp_filename, 'rt') as gf:
# gzip will fail next line if file is not gzipped
actual_content = gf.read()
assert expected_content == actual_content
finally:
if os.path.isfile(temp_filename):
os.unlink(temp_filename)
def test_gzipping_can_be_turned_off_even_for_dot_gz():
_filename = pybedtools.example_filename('a.bed')
with open(_filename) as f:
expected_content = f.read()
__, temp_filename = tempfile.mkstemp(suffix='.gz')
try:
bedtool = pybedtools.BedTool(_filename)
bedtool.saveas(fn=temp_filename, compressed=False)
with open(temp_filename) as non_gz_f:
# actual content will be jumbled if non_gz_f is unset
actual_content = non_gz_f.read()
assert expected_content == actual_content
finally:
if os.path.isfile(temp_filename):
os.unlink(temp_filename)
def test_gzipping_can_be_turned_off_even_for_dot_gz():
_filename = pybedtools.example_filename('a.bed')
with open(_filename) as f:
expected_content = f.read()
__, temp_filename = tempfile.mkstemp(suffix='.gz')
try:
bedtool = pybedtools.BedTool(_filename)
bedtool.saveas(fn=temp_filename, compressed=False)
with open(temp_filename) as non_gz_f:
# actual content will be jumbled if non_gz_f is unset
actual_content = non_gz_f.read()
assert_equal(expected_content, actual_content)
finally:
if os.path.isfile(temp_filename):
os.unlink(temp_filename)
def test_gzipping_is_default_when_extension_is_dot_gz():
_filename = pybedtools.example_filename('a.bed')
with open(_filename) as f:
expected_content = f.read()
__, temp_filename = tempfile.mkstemp(suffix='.gz')
try:
bedtool = pybedtools.BedTool(_filename)
bedtool.saveas(fn=temp_filename)
with gzip.open(temp_filename, 'rt') as gf:
# gzip will fail next line if file is not gzipped
actual_content = gf.read()
assert_equal(expected_content, actual_content)
finally:
if os.path.isfile(temp_filename):
os.unlink(temp_filename)
def test_bam_to_fastq():
x = pybedtools.example_bedtool('small.bam')
tmpfn = pybedtools.BedTool._tmp()
y = x.bam_to_fastq(fq=tmpfn)
assert open(y.fastq).read() == open(pybedtools.example_filename('small.fastq')).read()
def test_igv():
a = pybedtools.example_bedtool('a.bed')
a = a.igv()
obs = open(a.igv_script).read()
exp = open(pybedtools.example_filename('a.igv_script')).read()
assert obs == exp
conf['method'] = method
conf['method_kwargs'] = method_kwargs
conf.update(kwargs)
super(ConfiguredBedToolsDemo, self).__init__(**conf)
if __name__ == "__main__":
"""
bts = [
pybedtools.example_bedtool('BEAF_Kc_Bushey_2009.bed'),
pybedtools.example_bedtool('CTCF_Kc_Bushey_2009.bed'),
pybedtools.example_bedtool('Cp190_Kc_Bushey_2009.bed'),
pybedtools.example_bedtool('SuHw_Kc_Bushey_2009.bed'),
]
names = ['BEAF', 'CTCF', 'Cp190', 'Su(Hw)']
#bts = [
# pybedtools.example_bedtool('a.bed'),
# pybedtools.example_bedtool('b.bed')]
#names = ['a','b']
d, m = binary_heatmap(bts, names)
print binary_summary(d)
"""
conf_file = pybedtools.example_filename('democonfig.yaml')
data_path = pybedtools.example_filename("") # dir name
ax1 = ConfiguredBedToolsDemo(conf_file, method='intersect', method_kwargs={},
data_path=data_path).plot()
ax2 = ConfiguredBedToolsDemo(conf_file, method='intersect', method_kwargs=dict(u=True),
data_path=data_path).plot()
plt.show()
