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import pybedtools
from textwrap import dedent
from .tfuncs import setup_module, teardown_module
from pybedtools.scripts import annotate, venn_mpl, venn_gchart
import pytest
import subprocess as sp
import os
import sys
def test_annotate_main():
# exits after printing help when sys.argv is not as it should be.
orig_stderr = sys.stderr
sys.stderr = open('annotmp','w')
with pytest.raises(SystemExit):
annotate.main()
sys.stderr = orig_stderr
os.unlink('annotmp')
def test_annotate_closest():
a = pybedtools.example_bedtool('m1.bed')
b = pybedtools.example_bedtool('mm9.bed12')
c = annotate.add_closest(a, b)
assert len(a) == len(c), (len(a), len(c), str(c))
assert a.field_count() == c.field_count() - 2
# in this test-case, the final column should be exon;intron
# since m1 completely contains both an exon and an intron.
f = next(iter(c))
# waiting for fix to bedtools:
#assert f.fields[-1] == "exon;intron", f.fields[-1]
def test_annotate_xstream():
a = pybedtools.example_bedtool('m1.bed')
b = pybedtools.example_bedtool('mm9.bed12')
c = annotate.add_xstream(a, b, dist=1000, updown="up")
assert a.field_count() == c.field_count() - 1
assert len(a) == len(c)
d = annotate.add_xstream(c, b, dist=1000, updown="down")
assert a.field_count() == d.field_count() - 2
def test_venn_mpl():
"""
compares output image to expected
"""
try:
import matplotlib
except ImportError:
import sys
sys.stderr.write('Need matplotlib installed to test venn_mpl')
return
here = os.path.dirname(__file__)
expected_fn = os.path.join(here, 'mpl-expected.png')
original = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(pybedtools.BedTool(original[450:650]).saveas())
outfn = 'mplout.png'
venn_mpl.venn_mpl(a=a.fn, b=b.fn, c=c.fn, colors=['r','b','g'], outfn=outfn, labels=['a','b','c'])
# On a different machine, the created image is not visibly different but is
# numerically different. Not sure what a reasonable tolerance is, but this
# seems to work for now....
o = matplotlib.image.imread(outfn)
e = matplotlib.image.imread(expected_fn)
TOLERANCE = 200
SUM = abs((o - e).sum())
assert SUM < TOLERANCE, SUM
os.unlink(outfn)
def test_venn_gchart_data_is_correct():
original = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(pybedtools.BedTool(original[450:650]).saveas())
colors='00FF00,FF0000,0000FF'
labels = 'a,b,c'
expected_data = {'chco': '00FF00,FF0000,0000FF',
'chd': 't:1.0,0.4,0.7167,0.0667,0.05,0.1833,0.0167',
'chs': '300x300',
'cht': 'v',
'chdl': 'a|b|c'}
data = venn_gchart.venn_gchart(a=a.fn,
b=b.fn,
c=c.fn,
colors=colors.split(','),
labels=labels.split(','),
size='300x300')
for key in expected_data.keys():
e = expected_data[key]
o = data[key]
assert e == o
@pytest.mark.skip(
'Small differences between fonts in PNG are sometimes produced and need to be accounted for'
)
def test_venn_gchart_png_is_saved_correctly():
here = os.path.dirname(__file__)
expected = open(os.path.join(here, 'gchart-expected.png')).read()
original = pybedtools.example_bedtool('rmsk.hg18.chr21.small.bed').sort().merge()
a = pybedtools.BedTool(original[:300]).saveas()
b = pybedtools.BedTool(original[:20]).saveas().cat(pybedtools.BedTool(original[400:500]).saveas())
c = pybedtools.BedTool(original[15:30]).saveas().cat(pybedtools.BedTool(original[450:650]).saveas())
colors='00FF00,FF0000,0000FF'
outfn = 'gchart_out.png'
labels = 'a,b,c'
data = venn_gchart.venn_gchart(a=a.fn,
b=b.fn,
c=c.fn,
colors=colors.split(','),
labels=labels.split(','),
size='300x300')
venn_gchart.gchart(data, outfn)
assert_equal(open(outfn).read(), expected)
os.unlink(outfn)
def test_venn_mpl_main():
orig_stderr = sys.stderr
sys.stderr = open('mpltmp','w')
with pytest.raises(SystemExit):
venn_mpl.main()
sys.stderr = orig_stderr
os.unlink('mpltmp')
def test_venn_gchart_main():
orig_stderr = sys.stderr
sys.stderr = open('gcharttmp','w')
with pytest.raises(SystemExit):
venn_gchart.main()
sys.stderr = orig_stderr
os.unlink('gcharttmp')
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
""")
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