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 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 test_merge_single_ribo(self):
single_merged = h5py.File(BytesIO(), "w")
merge_ribos(single_merged, [self.handle])
self.assertTrue("merzifon" in get_experiment_names(single_merged))