def read10xCountsRaw(tenx_analysis, output):
tenx_analysis.load()
utils = DropletUtils()
counts = utils.read10xCounts(tenx_analysis.raw_matrices())
sce = SingleCellExperiment.fromRS4(counts)
sce.save(output)
return sce
def test_save_and_load_rdata(self):
print("Reading")
tenx = DropletUtils()
rs4_result = tenx.read10xCounts("/home/ceglian/data/raw_gene_bc_matrices/hg19/")
sce = SingleCellExperiment.fromRS4(rs4_result)
print("Writing")
sce.save("tests/sce_1.rdata")
print("Loading...")
sce_saved = SingleCellExperiment.fromRData("tests/sce_1.rdata")
print(sce_saved.assays["counts"].shape)
def test_symbol_retrieve(self):
tenx = TenxAnalysis("tests/pre_igo")
sce = TenX.read10xCounts(tenx)
print(sce.rowData.keys())
example_rda = os.path.join(base_dir, "tests/example_sce.rda")
sce = SingleCellExperiment.fromRData(example_rda)
print(sce.rowData.keys())
tenx = DropletUtils()
rs4_result = tenx.read10xCounts("tests/hg19/")
sce = SingleCellExperiment.fromRS4(rs4_result)
print(sce.rowData.keys())
example_rda = os.path.join(base_dir, "tests/example_copy_number.rda")
sce = SingleCellExperiment.fromRData(example_rda)
print(sce.rowData.keys())
print(sce.rownames)
print(sce.colnames)
def normalizeExprs(self, sce):
res = self._normalizeExprs(sce)
return SingleCellExperiment.fromRS4(res)
def calculateQCMetrics(self, sce):
res = self._calculateQCMetrics(sce)
return SingleCellExperiment.fromRS4(res)
def read10xCounts(path, output):
utils = DropletUtils()
counts = utils.read10xCounts(path)
sce = SingleCellExperiment.fromRS4(counts)
sce.save(output)
return sce
def test_get_assay_with_row_col_data_rs4(self):
tenx = DropletUtils()
rs4_results = tenx.read10xCounts(
"/home/ceglian/data/raw_gene_bc_matrices/hg19/")
sce_from_rs4 = SingleCellExperiment.fromRS4(rs4_results)
def test_read10x_counts_load_rs4(self):
tenx = DropletUtils()
rs4_result = tenx.read10xCounts(
"/home/ceglian/data/raw_gene_bc_matrices/hg19/")
sce_from_rs4 = SingleCellExperiment.fromRS4(rs4_result)
def read10xCountsFiltered(tenx_analysis, output):
utils = DropletUtils()
counts = utils.read10xCounts(tenx_analysis.filtered_matrices())
sce = SingleCellExperiment.fromRS4(counts)
sce.save(output)
return sce
def read10xCounts(tenx_analysis):
utils = DropletUtils()
counts = utils.read10xCounts(tenx_analysis.raw_matrices(config.build))
sce = SingleCellExperiment.fromRS4(counts)
return sce