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import os
import filecmp
from matplotlib.testing.compare import compare_images
from tempfile import NamedTemporaryFile
import deeptools.plotCoverage
import deeptools.utilities
__author__ = 'Bjoern'
TEST_DATA = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_plotCoverage/"
tolerance = 13 # default matplotlib pixed difference tolerance
def test_plotCoverage_default():
plotfile = NamedTemporaryFile(suffix='.png', prefix='deeptools_testfile_', delete=False)
txtfile = NamedTemporaryFile(suffix='.tab', prefix='deeptools_testfile_', delete=False)
for fmat in ["bam", "cram"]:
args = "--bamfiles {0}test1.{3} {0}test2.{3} --plotFile {1}" \
" --plotFileFormat png --outRawCounts {2}".format(TEST_DATA, plotfile.name, txtfile.name, fmat).split()
deeptools.plotCoverage.main(args)
if fmat == "bam":
assert filecmp.cmp(os.path.join(ROOT, 'outRawCounts_default.tabular'), txtfile.name) is True
res = compare_images(ROOT + 'plotCoverage_default.png', plotfile.name, tolerance)
assert res is None, res
os.remove(txtfile.name)
os.remove(plotfile.name)
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