def setUp(self, rename_func=None):
self.tmp_files = list()
self.ref_len_file = StringIO(TRANSCRIPT_LENGTHS)
self.annotation_file = StringIO(TRANSCRIPT_ANNOTATION)
self.alignment_file_1 = StringIO(READ_SET_1)
self.alignment_file_2 = StringIO(READ_SET_2)
self.handle = h5py.File(BytesIO(), "w")
self.handle_2 = h5py.File(BytesIO(), "w")
create.create_ribo(ribo=self.handle,
experiment_name="merzifon",
alignment_file=self.alignment_file_1,
reference_name="hg38",
lengths_file=self.ref_len_file,
annotation_file=self.annotation_file,
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
length_min=2,
length_max=5,
store_coverage=False,
nprocess=NPROCESS,
tmp_file_prefix="")
self.ref_len_file.seek(0)
self.annotation_file.seek(0)
self.alignment_file_1 = StringIO(READ_SET_1)
set_metadata(self.handle, "merzifon", METADATA_EXPERIMENT_DICT)
create.create_ribo(ribo=self.handle_2,
experiment_name="ankara",
alignment_file=self.alignment_file_2,
reference_name="hg38",
lengths_file=self.ref_len_file,
annotation_file=self.annotation_file,
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
length_min=2,
length_max=5,
store_coverage=True,
nprocess=NPROCESS,
tmp_file_prefix="")
self.ref_len_file.seek(0)
self.annotation_file.seek(0)
self.alignment_file_2 = StringIO(READ_SET_2)
self.merged_io = BytesIO()
self.merged_ribo = h5py.File(self.merged_io, "w")
merge_ribos(self.merged_ribo, [self.handle, self.handle_2])
set_metadata(self.merged_ribo, name=None, metadata=RIBO_METADATA_STR_1)
self.merged_ribo.close()
self.sample_ribo = Ribo(self.merged_io, alias=rename_func)
def setUp(self):
self.tmp_files = list()
self.ref_len_file = StringIO(TRANSCRIPT_LENGTHS)
self.annotation_file = StringIO(TRANSCRIPT_ANNOTATION)
self.alignment_file_1 = StringIO(READ_SET_1)
self.alignment_file_2 = StringIO(READ_SET_2)
self.in_ref_len_file = StringIO(INCOMPATIBLE_TRANSCRIPT_LENGTHS)
self.in_annotation_file = StringIO(INCOMPATIBLE_TRANSCRIPT_ANNOTATION)
self.handle = h5py.File(BytesIO(), "w")
self.handle_2 = h5py.File(BytesIO(), "w")
create.create_ribo(ribo=self.handle,
experiment_name="merzifon",
alignment_file=self.alignment_file_1,
reference_name="hg38",
lengths_file=self.ref_len_file,
annotation_file=self.annotation_file,
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
length_min=2,
length_max=5,
nprocess=NPROCESS,
tmp_file_prefix="")
self.ref_len_file.seek(0)
self.annotation_file.seek(0)
self.alignment_file_1 = StringIO(READ_SET_1)
create.create_ribo(ribo=self.handle_2,
experiment_name="ankara",
alignment_file=self.alignment_file_2,
reference_name="hg38",
lengths_file=self.ref_len_file,
annotation_file=self.annotation_file,
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
length_min=2,
length_max=5,
nprocess=NPROCESS,
tmp_file_prefix="")
self.ref_len_file.seek(0)
self.annotation_file.seek(0)
self.alignment_file_2 = StringIO(READ_SET_2)
self.merged_ribo = h5py.File(BytesIO(), "w")
merge_ribos(self.merged_ribo, [self.handle, self.handle_2])
def setUp(self):
self.ref_len_file = StringIO(TRANSCRIPT_LENGTHS)
self.annotation_file = StringIO(TRANSCRIPT_ANNOTATION)
self.alignment_file = StringIO(READ_SET_1)
self.alignment_file_2 = StringIO(READ_SET_2)
self.tsv_1 = StringIO(rnaseq_data.RNASEQ_tsv_1)
self.tsv_2 = StringIO(rnaseq_data.RNASEQ_tsv_2)
self.tsv_3 = StringIO(rnaseq_data.RNASEQ_tsv_3)
self.handle = h5py.File(BytesIO(), "w")
self.handle_2 = h5py.File(BytesIO(), "w")
self.rnaseq_reads_handle = StringIO(rnaseq_data.RNASEQ_READS)
self.rnaseq_reads_handle_2 = StringIO(rnaseq_data.RNASEQ_READS_2)
create.create_ribo(self.handle,
"merzifon",
alignment_file=self.alignment_file,
reference_name="appris_human_v2",
length_min=2,
length_max=5,
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
lengths_file=self.ref_len_file,
store_coverage=True,
annotation_file=self.annotation_file)
self.ref_len_file.seek(0)
self.annotation_file.seek(0)
create.create_ribo(self.handle_2,
"adana",
alignment_file=self.alignment_file_2,
reference_name="appris_human_v2",
length_min=2,
length_max=5,
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
lengths_file=self.ref_len_file,
store_coverage=True,
annotation_file=self.annotation_file)
self.merged_ribo = h5py.File(BytesIO(), "w")
merge_ribos(self.merged_ribo, [self.handle, self.handle_2])
def setUp(self):
self.ref_len_file = StringIO(TRANSCRIPT_LENGTHS)
self.annotation_file = StringIO(TRANSCRIPT_ANNOTATION)
self.alignment_file = StringIO(READ_SET_1)
self.handle = h5py.File(BytesIO(), "w")
create.create_ribo(self.handle,
experiment_name="merzifon",
alignment_file=self.alignment_file,
metagene_radius=3,
length_min=2,
length_max=5,
left_span=3,
right_span=2,
reference_name="appris_human_v2",
lengths_file=self.ref_len_file,
annotation_file=self.annotation_file)
def setUp(self):
self.len_file = StringIO(TRANSCRIPT_LENGTHS)
self.annotation_file = StringIO(TRANSCRIPT_ANNOTATION)
self.alignment_file = StringIO(READ_SET_1)
self.handle = h5py.File(BytesIO(), "w")
create.create_ribo(self.handle,
experiment_name = "merzifon",
alignment_file = self.alignment_file,
reference_name = "hg38",
lengths_file = self.len_file,
annotation_file = self.annotation_file,
metagene_radius = METAGENE_RADIUS,
left_span = LEFT_SPAN, right_span = RIGHT_SPAN,
length_min = 2, length_max = 5,
tmp_file_prefix = "")
def setUp(self):
self.ref_len_file = StringIO(TRANSCRIPT_LENGTHS)
self.annotation_file = StringIO(TRANSCRIPT_ANNOTATION)
self.alignment_file = StringIO(READ_SET_1)
self.handle = h5py.File(BytesIO(), "w")
create.create_ribo(self.handle,
"merzifon",
alignment_file=self.alignment_file,
reference_name="appris_human_v2",
length_min=2,
length_max=5,
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
lengths_file=self.ref_len_file,
store_coverage=True,
annotation_file=self.annotation_file)
def setUp(self):
super().setUp()
self.file_handle_3 = BytesIO()
self.ribo_handle_3 = h5py.File(self.file_handle_3, "w")
create.create_ribo(ribo=self.ribo_handle_3,
experiment_name="adana",
alignment_file=self.alignment_file_1,
reference_name="hg38",
lengths_file=self.ref_len_file,
annotation_file=self.annotation_file,
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
length_min=2,
length_max=5,
store_coverage=True,
nprocess=1,
tmp_file_prefix="")
self.ribo_handle_3.close()
self.adana_ribo = Ribo(self.file_handle_3)
def test_merge_incompatible_reference(self):
handle_incompatible = h5py.File(BytesIO(), "w")
ribo_out = h5py.File(BytesIO(), "w")
create.create_ribo(
ribo=handle_incompatible,
experiment_name="izmir",
alignment_file=self.alignment_file_2,
reference_name="hg38",
lengths_file=self.in_ref_len_file, # incomp lens
annotation_file=self.in_annotation_file, # incomp annot.
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
length_min=2,
length_max=5,
nprocess=NPROCESS,
tmp_file_prefix="")
with self.assertRaises(ValueError):
merge_ribos(ribo_out,
[self.handle, self.handle_2, handle_incompatible])
def setUp(self):
self.tmp_files = list()
self.ref_len_file = StringIO(GENERIC_TRANSCRIPT_LENGTHS)
self.annotation_file = StringIO(GENERIC_TRANSCRIPT_ANNOTATION)
self.alignment_file_1 = StringIO(READ_SET_1)
self.alignment_file_2 = StringIO(READ_SET_2)
self.handle_io = BytesIO()
self.handle = h5py.File(self.handle_io, "w")
self.handle_2 = h5py.File(BytesIO(), "w")
self.h5_handle = h5py.File(BytesIO(), "w")
initialize(self.h5_handle,
experiment_name="dummy",
reference_name="test_ref")
(ref_names, ref_lengths) = \
set_reference_names_and_lengths(self.h5_handle , self.ref_len_file)
self.ref_len_file.seek(0)
self.annotation_lines = GENERIC_TRANSCRIPT_ANNOTATION.split("\n")
create.create_ribo(ribo=self.handle,
experiment_name="experiment-1",
alignment_file=self.alignment_file_1,
reference_name="hg38",
lengths_file=self.ref_len_file,
annotation_file=self.annotation_file,
metagene_radius=METAGENE_RADIUS,
left_span=LEFT_SPAN,
right_span=RIGHT_SPAN,
length_min=LENGTH_MIN,
length_max=LENGTH_MAX,
store_coverage=True,
nprocess=NPROCESS,
tmp_file_prefix="")
self.handle.close()
self.sample_ribo = Ribo(self.handle_io)
# Get the region counts
self.cds_counts = \
self.sample_ribo.get_region_counts( region_name = CDS_name,
sum_references = False)
self.utr5_counts = \
self.sample_ribo.get_region_counts( region_name = UTR5_name,
sum_references = False)
self.utr3_counts = \
self.sample_ribo.get_region_counts( region_name = UTR3_name,
sum_references = False)
self.utr5j_counts = \
self.sample_ribo.get_region_counts( region_name = UTR5_JUNCTION_name,
sum_references = False)
self.utr3j_counts = \
self.sample_ribo.get_region_counts( region_name = UTR3_JUNCTION_name,
sum_references = False)