def test_build_gctoo(self):
filepath = "functional_tests/test_assemble/test_write_output_gct.txt"
if os.path.exists(filepath):
os.remove(filepath)
prn = "my_prism_replicate"
pert_list = []
p = prism_metadata.Perturbagen()
p.pert_well = "J01"
p.pert_id = "BRD-K12345678"
p.pert_dose = 11.0
p.pert_dose_unit = "uM"
pert_list.append(p)
p = prism_metadata.Perturbagen()
p.pert_well = "M03"
p.pert_id = "BRD-K91011121"
p.pert_dose = 13.0
p.pert_dose_unit = "mg/mL"
pert_list.append(p)
p = prism_metadata.Perturbagen()
p.pert_well = "B02"
p.pert_id = "BRD-K31415171"
p.pert_dose = 17.0
p.pert_dose_unit = "nM"
pert_list.append(p)
cell_list = []
c = prism_metadata.PrismCell(pool_id="fake pool",
analyte_id="fake analyte",
davepool_id="fake davepool",
feature_id='c-3')
cell_list.append(c)
c = prism_metadata.PrismCell(pool_id="fake pool 2",
analyte_id="fake analyte 2",
davepool_id="fake davepool 2",
feature_id='c-5')
cell_list.append(c)
c = prism_metadata.PrismCell(pool_id="fake pool 2",
analyte_id="fake analyte 3",
davepool_id="fake davepool 2",
feature_id='c-7')
cell_list.append(c)
data_by_cell = assemble_core.DataByCell(
{
cell_list[1]: [1, 2, 11],
cell_list[2]: [13, 17, 19],
cell_list[0]: [23, 29, 31]
}, ["J01", "M03", "B02"])
r = assemble_core.build_gctoo(prn, pert_list, data_by_cell)
self.assertIsNotNone(r)
logger.debug("r: {}".format(r))
logger.debug("r.col_metadata_df: {}".format(r.col_metadata_df))
logger.debug("r.row_metadata_df: {}".format(r.row_metadata_df))
logger.debug("r.data_df: {}".format(r.data_df))
def test_convert_objects_to_metadata_df_for_prism_cell(self):
cell_list = [pm.PrismCell(1, 2, 3, 5), pm.PrismCell(7, 11, 13, 17)]
def index_builder(c):
return c.id
r = pm.convert_objects_to_metadata_df(index_builder, cell_list)
assert r is not None
logger.debug("r: {}".format(r))
assert "pool_id" in r.columns
assert "davepool_id" in r.columns
assert "analyte_id" in r.columns
def test_build_davepool_to_cells_map(self):
l = [
prism_metadata.PrismCell(pool_id=str(x + 20),
analyte_id=str(x + 10),
davepool_id=str(x / 2)) for x in range(6)
]
logger.debug("l: {}".format(l))
r = assemble_core.build_davepool_id_to_cells_map(l)
assert len(r) == 3, len(r)
logger.debug("r: {}".format(r))
for x in range(3):
y = str(x)
assert y in r, y
assert len(r[y]) == 2, r[y]
def test_build_data_by_cell(self):
cells = [
prism_metadata.PrismCell(pool_id=str(x + 20),
analyte_id=str(x + 10),
davepool_id=str(x / 2)) for x in range(2)
]
logger.debug("cells: {}".format(cells))
davepool_data_obj = davepool_data.DavepoolData()
davepool_data_obj.median_headers = ["Location", "10", "11"]
davepool_data_obj.median_headers.extend(
[str(x) for x in range(30, 40)])
davepool_data_obj.median_data = {"A01": [1, 2], "J13": [3, 5]}
davepool_data_obj.median_data['A01'].extend([x for x in range(40, 50)])
davepool_data_obj.median_data['J13'].extend([x for x in range(50, 60)])
davepool_data_obj.count_headers = davepool_data_obj.median_headers
davepool_data_obj.count_data = {"B03": [7, 11], "L17": [13, 17]}
davepool_data_obj.count_data["B03"].extend([x for x in range(60, 70)])
davepool_data_obj.count_data["L17"].extend([x for x in range(70, 80)])
logger.debug("davepool_data_obj: {}".format(davepool_data_obj))
rep = assemble_core.build_data_by_cell(cells, davepool_data_obj)
r_med = rep[0]
assert r_med is not None
logger.debug("r_med: {}".format(r_med))
assert r_med.well_list is not None
assert len(r_med.well_list) == 2, len(r_med.well_list)
assert "A01" in r_med.well_list, r_med.well_list
assert "J13" in r_med.well_list, r_med.well_list
assert len(r_med.cell_data_map) == len(cells), (len(
r_med.cell_data_map), len(cells))
r_count = rep[1]
assert len(r_count.well_list) == 2, len(r_count.well_list)
logger.debug("r_count.well_list: {}".format(r_count.well_list))
assert "B03" in r_count.well_list, r_count.well_list
assert "L17" in r_count.well_list, r_count.well_list
assert len(r_count.cell_data_map) == len(cells), (len(
r_count.cell_data_map), len(cells))
logger.debug("r_count.cell_data_map: {}".format(
r_count.cell_data_map))
def test___init__(self):
r = pm.PrismCell()
assert hasattr(r, "pool_id")
assert hasattr(r, "analyte_id")
def test_process_data(self):
cells = [
prism_metadata.PrismCell(pool_id=str(x + 20),
analyte_id=str(x + 10),
davepool_id=str(x / 2)) for x in range(4)
]
logger.debug("cells: {}".format(cells))
cells_map = assemble_core.build_davepool_id_to_cells_map(cells)
logger.debug("cells_map: {}".format(cells_map))
davepool_list = []
davepool_data_obj = davepool_data.DavepoolData()
davepool_list.append(davepool_data_obj)
davepool_data_obj.davepool_id = "0"
davepool_data_obj.median_headers = [str(x) for x in range(10, 22)]
davepool_data_obj.median_headers.insert(0, "Location")
davepool_data_obj.median_data = {"A01": [1, 2], "J13": [3, 5]}
davepool_data_obj.median_data["A01"].extend([x for x in range(40, 50)])
davepool_data_obj.median_data["J13"].extend([x for x in range(50, 60)])
davepool_data_obj.count_headers = davepool_data_obj.median_headers
davepool_data_obj.count_data = {"A01": [7, 11], "J13": [13, 17]}
davepool_data_obj.count_data["A01"].extend([x for x in range(60, 70)])
davepool_data_obj.count_data["J13"].extend([x for x in range(70, 80)])
logger.debug("davepool_data_obj: {}".format(davepool_data_obj))
davepool_data_obj = davepool_data.DavepoolData()
davepool_list.append(davepool_data_obj)
davepool_data_obj.davepool_id = "1"
davepool_data_obj.median_headers = [str(x) for x in range(10, 22)]
davepool_data_obj.median_headers.insert(0, "Location")
davepool_data_obj.median_data = {
"A01": [-1, -2, 19, 23],
"J13": [-3, -5, 29, 31]
}
davepool_data_obj.median_data["A01"].extend([x for x in range(80, 88)])
davepool_data_obj.median_data["J13"].extend([x for x in range(90, 98)])
davepool_data_obj.count_headers = davepool_data_obj.median_headers
davepool_data_obj.count_data = {
"A01": [-7, -11, 37, 41],
"J13": [-13, -17, 43, 47]
}
davepool_data_obj.count_data["A01"].extend(
[x for x in range(100, 108)])
davepool_data_obj.count_data["J13"].extend(
[x for x in range(110, 118)])
logger.debug("davepool_data_obj: {}".format(davepool_data_obj))
r = assemble_core.process_data(davepool_list, cells_map)
assert len(r) == 2, len(r)
median_data_by_cell = r[0]
assert median_data_by_cell is not None
logger.debug("median_data_by_cell: {}".format(median_data_by_cell))
assert 2 == median_data_by_cell.cell_data_map[cells[1]][0]
assert 3 == median_data_by_cell.cell_data_map[cells[0]][1]
t_wells = median_data_by_cell.well_list
logger.debug("t_wells: {}".format(t_wells))
assert "J13" in t_wells
assert 23 == median_data_by_cell.cell_data_map[cells[3]][0]
assert 29 == median_data_by_cell.cell_data_map[cells[2]][1]