def test_seqplot(self):
''' test that we can make plots
'''
folder = os.path.dirname(__file__)
path = os.path.join(folder, 'data', 'example.bam')
fasta = os.path.join(folder, 'data', 'reference.fasta')
# check that we make a plot with the correct image. check this by
# returning png data, then getting the sha1 digest. This will fail if
# a single bit chenges, so perhaps this is too stringent.
data = seqplot([path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta)
checksum = hashlib.sha1(data).hexdigest()
# now try writing a plot to PNG file.
single = tempfile.NamedTemporaryFile(suffix='.png')
seqplot([path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta,
out=single.name)
self.assertTrue(os.path.getsize(single.name) > 0)
# check we have written the same data as would be returned
with open(single.name, 'rb') as handle:
singlechecksum = hashlib.sha1(handle.read()).hexdigest()
self.assertEqual(checksum, singlechecksum)
# now check we can plot multiple sequence files in a single image
double = tempfile.NamedTemporaryFile(suffix='.png')
seqplot([path, path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta,
out=double.name)
self.assertTrue(
os.path.getsize(double.name) > os.path.getsize(single.name))
# check that the sha1 hash does not match the earlier one. this may
# be excessive.
with open(double.name, 'rb') as handle:
doublechecksum = hashlib.sha1(handle.read()).hexdigest()
self.assertNotEqual(singlechecksum, doublechecksum)
def test_seqplot_png(self):
''' test that a seqplot PNG is the right shape
'''
folder = os.path.dirname(__file__)
path = os.path.join(folder, 'data', 'example.bam')
fasta = os.path.join(folder, 'data', 'reference.fasta')
first = tempfile.NamedTemporaryFile(suffix='.png')
seqplot([path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta,
out=first.name)
# test basic characteristics of the written png
with Image.open(first.name) as im:
self.assertEqual(im.size, (4000, 615))
def test_seqplot_cram(self):
''' test that we can plot from CRAM files
'''
folder = os.path.dirname(__file__)
path = os.path.join(folder, 'data', 'example.cram')
fasta = os.path.join(folder, 'data', 'reference.fasta')
single = tempfile.NamedTemporaryFile(suffix='.png')
seqplot([path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta,
out=single.name)
# check that we have written some data to the file
self.assertTrue(os.path.getsize(single.name) > 0)
def test_seqplot_by_strand(self):
''' test that we can plot bam, and color reads by strand
'''
folder = os.path.dirname(__file__)
path = os.path.join(folder, 'data', 'example.bam')
fasta = os.path.join(folder, 'data', 'reference.fasta')
# check that we can plot by strand
data = seqplot([path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta,
by_strand=True)
checksum = hashlib.sha1(data).hexdigest()
data = seqplot([path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta)
checksum_unstranded = hashlib.sha1(data).hexdigest()
self.assertNotEqual(checksum, checksum_unstranded)
def test_seqplot(self):
''' test that we can make plots
'''
folder = os.path.dirname(__file__)
path = os.path.join(folder, 'data', 'example.bam')
fasta = os.path.join(folder, 'data', 'reference.fasta')
# check that we make a plot with the correct image. check this by
# returning png data, then getting the sha1 digest. This will fail if
# a single bit chenges, so perhaps this is too stringent.
first = tempfile.NamedTemporaryFile(suffix='.png')
seqplot([path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta,
out=first.name)
# test we don't get the empty file checksum, the file has some content
self.assertNotEqual(checksum_file(first.name),
'da39a3ee5e6b4b0d3255bfef95601890afd80709')
# now try writing a plot to PNG file.
single = tempfile.NamedTemporaryFile(suffix='.png')
seqplot([path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta,
out=single.name)
self.assertTrue(os.path.getsize(single.name) > 0)
# check we have written the same data between runs
self.assertEqual(checksum_file(first.name), checksum_file(single.name))
# now check we can plot multiple sequence files in a single image
double = tempfile.NamedTemporaryFile(suffix='.png')
seqplot([path, path],
chrom='1',
start=30000,
end=30400,
fastafile=fasta,
out=double.name)
self.assertTrue(
os.path.getsize(double.name) > os.path.getsize(single.name))
# check that the sha1 hash does not match the earlier one. this may
# be excessive.
self.assertNotEqual(checksum_file(single.name),
checksum_file(double.name))