def setUp(self):
if not pysam.config.HAVE_LIBCURL or not check_url(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 check_url(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 check_url(self.url):
return
try:
with pysam.Fastafile(self.url) as f:
self.assertEqual(len(f.fetch("chr1", 0, 1000)), 1000)
except (OSError, IOError):
pass
def test_sequence_lengths_are_available(self):
if not check_url(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 testFTPView(self):
if not check_url(self.url):
return
with pysam.Fastafile(self.url) as f:
self.assertEqual(len(f.fetch("chr1", 0, 1000)), 1000)