def setUp(self):
if not pysam.config.HAVE_LIBCURL or not checkURL(self.url):
self.remote_file = None
else:
self.remote_file = pysam.TabixFile(self.url, "r")
self.local_file = pysam.TabixFile(self.local, "r")
def setUp(self):
if not checkURL(self.url):
self.remote_file = None
return
self.remote_file = pysam.TabixFile(self.url, "r")
self.local_file = pysam.TabixFile(self.local, "r")
def testFTPView(self):
if not checkURL(self.url):
return
with pysam.Fastafile(self.url) as f:
self.assertEqual(
len(f.fetch("chr1", 0, 1000)),
1000)
def setUp(self):
if not checkURL(self.url):
self.remote_file = None
return
self.remote_file = pysam.TabixFile(self.url, "r")
self.local_file = pysam.TabixFile(self.local, "r")
def setUp(self):
if not pysam.config.HAVE_LIBCURL or not checkURL(self.url):
self.remote_file = None
else:
self.remote_file = pysam.TabixFile(self.url, "r")
self.local_file = pysam.TabixFile(self.local, "r")
def testFTPView(self):
if not checkURL(self.url):
return
f = pysam.Fastafile(self.url)
self.assertEqual(
len(f.fetch("chr1", 0, 1000)),
1000)
def test_sequence_lengths_are_available(self):
if not checkURL(self.url):
return
with pysam.Fastafile(self.url) as f:
self.assertEqual(len(f.references), 3366)
self.assertTrue("chr1" in f.references)
self.assertEqual(f.lengths[0], 248956422)
self.assertEqual(f.get_reference_length("chr1"), 248956422)
def testFetchAll(self):
if not checkURL(self.url):
return
remote_result = list(self.remote_file.fetch())
local_result = list(self.local_file.fetch())
self.assertEqual(len(remote_result), len(local_result))
for x, y in zip(remote_result, local_result):
self.assertEqual(x, y)
def testFetchAll(self):
if not checkURL(self.url):
return
remote_result = list(self.remote_file.fetch())
local_result = list(self.local_file.fetch())
self.assertEqual(len(remote_result), len(local_result))
for x, y in zip(remote_result, local_result):
self.assertEqual(x, y)
def test_sequence_lengths_are_available(self):
if not checkURL(self.url):
return
with pysam.Fastafile(self.url) as f:
self.assertEqual(len(f.references), 3366)
self.assertTrue("chr1" in f.references)
self.assertEqual(f.lengths[0],
248956422)
self.assertEqual(f.get_reference_length("chr1"),
248956422)
