class TestRNASEQ_2(ApiTestBase):
def setUp(self):
super().setUp()
# We need to init the ribo object in write mode
# Because we are going to add tnaseq data to it.
self.sample_ribo = Ribo(self.merged_io, file_mode="r+")
self.rnaseq_file_1 = StringIO(RNASEQ_READS)
self.rnaseq_file_2 = StringIO(RNASEQ_READS_2)
set_rnaseq(ribo_handle=self.sample_ribo._handle,
name="merzifon",
rnaseq_reads=self.rnaseq_file_1,
format="bed",
rnaseq_counts=None)
set_rnaseq(ribo_handle=self.sample_ribo._handle,
name="ankara",
rnaseq_reads=self.rnaseq_file_2,
format="bed",
rnaseq_counts=None)
# We need to re-initialize the ribo object
# so that the changes take effect.
self.sample_ribo._handle.close()
self.sample_ribo = Ribo(self.merged_io, file_mode="r+")
def test_has_rnaseq(self):
self.assertTrue(self.sample_ribo.has_rnaseq("merzifon"))
self.assertTrue(self.sample_ribo.has_rnaseq("ankara"))
def test_get_rnaseq_multiple(self):
rnaseq_df = self.sample_ribo.get_rnaseq()
self.assertTrue(
np.allclose([1, 0, 2, 1, 3], rnaseq_df.loc["merzifon", "GAPDH"]))
self.assertTrue(
np.allclose([0, 1, 3, 0, 1], rnaseq_df.loc["merzifon", "VEGFA"]))
self.assertTrue(
np.allclose([0, 1, 0, 0, 2], rnaseq_df.loc["merzifon", "MYC"]))
self.assertTrue(
np.isclose(rnaseq_df.loc["merzifon", "GAPDH"][CDS_name], 2))
self.assertTrue(
np.allclose([0, 0, 0, 0, 0], rnaseq_df.loc["ankara", "GAPDH"]))
self.assertTrue(
np.allclose([0, 0, 0, 2, 0], rnaseq_df.loc["ankara", "VEGFA"]))
self.assertTrue(
np.allclose([0, 0, 0, 0, 0], rnaseq_df.loc["ankara", "MYC"]))
self.assertTrue(
np.isclose(rnaseq_df.loc["ankara", "VEGFA"][UTR3_JUNCTION_name],
2))
class TestRNASEQ(ApiTestBase):
def setUp(self):
super().setUp()
# We need to init the ribo object in write mode
# Because we are going to add tnaseq data to it.
self.sample_ribo = Ribo(self.merged_io, file_mode="r+")
self.rnaseq_file_1 = StringIO(RNASEQ_READS)
self.rnaseq_file_2 = StringIO(RNASEQ_READS_2)
set_rnaseq(ribo_handle=self.sample_ribo._handle,
name="merzifon",
rnaseq_reads=self.rnaseq_file_1,
format="bed",
rnaseq_counts=None)
# We need to re-initialize the ribo object
# so that the changes take effect.
self.sample_ribo._handle.close()
self.sample_ribo = Ribo(self.merged_io, file_mode="r+")
def test_has_rnaseq(self):
self.assertTrue(self.sample_ribo.has_rnaseq("merzifon"))
self.assertTrue(not self.sample_ribo.has_rnaseq("ankara"))
def test_rnaseq_info(self):
self.assertTrue(self.sample_ribo.\
info["experiments"]["merzifon"]["RNA-Seq"])
self.assertTrue(not self.sample_ribo.\
info["experiments"]["ankara"]["RNA-Seq"])
def test_get_rnaseq_single(self):
rnaseq_df = self.sample_ribo.get_rnaseq("merzifon")
self.assertTrue(
np.allclose([1, 0, 2, 1, 3], rnaseq_df.loc["merzifon", "GAPDH"]))
self.assertTrue(
np.allclose([0, 1, 3, 0, 1], rnaseq_df.loc["merzifon", "VEGFA"]))
self.assertTrue(
np.allclose([0, 1, 0, 0, 2], rnaseq_df.loc["merzifon", "MYC"]))
self.assertTrue(
np.isclose(rnaseq_df.loc["merzifon", "GAPDH"][CDS_name], 2))
def test_get_rnaseq_from_nornaseq_exp(self):
with self.assertRaises(NORNASEQ) as exception_context:
rnaseq_df = self.sample_ribo.get_rnaseq("ankara")