def check(self, filename, raises=None):
with pysam.TabixFile(filename) as tf:
ref = load_and_convert(filename)
if raises is None:
self.assertEqual(len(list(tf.fetch())), len(ref))
else:
self.assertRaises(raises, tf.fetch)
def check(self, filename, raises=None):
with pysam.TabixFile(filename) as tf:
ref = load_and_convert(filename)
if raises is None:
self.assertEqual(len(list(tf.fetch())), len(ref))
else:
self.assertRaises(raises, tf.fetch)
def setUp(self):
self.tabix = pysam.TabixFile(self.filename)
self.compare = load_and_convert(self.filename)
self.tmpfilename_uncompressed = 'tmp_TestIterators'
with gzip.open(self.filename, "rb") as infile, \
open(self.tmpfilename_uncompressed, "wb") as outfile:
outfile.write(infile.read())
def setUp(self):
self.tabix = pysam.TabixFile(self.filename)
self.compare = load_and_convert(self.filename)
self.tmpfilename_uncompressed = 'tmp_TestIterators'
with gzip.open(self.filename, "rb") as infile, \
open(self.tmpfilename_uncompressed, "wb") as outfile:
outfile.write(infile.read())
def setUp(self):
self.tabix = pysam.TabixFile(self.filename)
self.compare = load_and_convert(self.filename)
def setUp(self):
self.compare = load_and_convert(os.path.join(CBCF_DATADIR,
self.filename),
encode=False)
def setUp(self):
self.tabix = pysam.TabixFile(self.filename)
self.compare = load_and_convert(self.filename)
def setUp(self):
TestVCF.setUp(self)
self.compare = load_and_convert(self.filename, encode=False)
def setUp(self):
TestVCF.setUp(self)
self.tabix = pysam.TabixFile(self.tmpfilename + ".gz")
self.compare = load_and_convert(self.filename)
def setUp(self):
self.compare = load_and_convert(
os.path.join(CBCF_DATADIR, self.filename),
encode=False)
def setUp(self):
TestVCF.setUp(self)
self.vcf = pysam.VCF()
self.compare = load_and_convert(self.filename, encode=False)
def setUp(self):
TestVCF.setUp(self)
self.tabix = pysam.TabixFile(self.tmpfilename + ".gz")
self.compare = load_and_convert(self.filename)
