def test_set_cell_count_project_missing_library_type(self):
"""
set_cell_count_for_project: test for scRNA-seq when library not set
"""
# Set up mock project with library type not set
project_dir = self._make_mock_analysis_project(
"10xGenomics Chromium 3'v3", None)
# Add metrics_summary.csv
counts_dir = os.path.join(project_dir, "qc", "cellranger_count",
"5.0.1", "refdata-gex-GRCh38-2020-A", "PJB1",
"outs")
mkdirs(counts_dir)
metrics_summary_file = os.path.join(counts_dir, "metrics_summary.csv")
with open(metrics_summary_file, 'w') as fp:
fp.write(METRICS_SUMMARY)
# Add QC info file
with open(os.path.join(project_dir, "qc", "qc.info"), 'wt') as fp:
fp.write(
"""Cellranger reference datasets\t/data/refdata-gex-GRCh38-2020-A
Cellranger version\t5.0.1
""")
# Check initial cell count
print("Checking number of cells")
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, None)
# Update the cell counts
print("Updating number of cells")
set_cell_count_for_project(project_dir)
# Check updated cell count
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, 2272)
def test_set_cell_count_for_multiome_gex_project(self):
"""
set_cell_count_for_project: test for single cell multiome GEX
"""
# Set up mock project
project_dir = self._make_mock_analysis_project(
"10xGenomics Single Cell Multiome", "GEX")
# Add metrics_summary.csv
counts_dir = os.path.join(project_dir, "qc", "cellranger_count",
"1.0.0",
"refdata-cellranger-arc-GRCh38-2020-A",
"PJB1", "outs")
mkdirs(counts_dir)
summary_file = os.path.join(counts_dir, "summary.csv")
with open(summary_file, 'w') as fp:
fp.write(MULTIOME_SUMMARY)
# Add QC info file
with open(os.path.join(project_dir, "qc", "qc.info"), 'wt') as fp:
fp.write(
"""Cellranger reference datasets\t/data/refdata-cellranger-arc-GRCh38-2020-A
Cellranger version\t1.0.0
""")
# Check initial cell count
print("Checking number of cells")
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, None)
# Update the cell counts
print("Updating number of cells")
set_cell_count_for_project(project_dir)
# Check updated cell count
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, 744)
def test_set_cell_count_for_atac_project_2_0_0(self):
"""
set_cell_count_for_project: test for scATAC-seq (Cellranger ATAC 2.0.0)
"""
# Set up mock project
project_dir = self._make_mock_analysis_project(
"10xGenomics Single Cell ATAC", "scATAC-seq")
# Add metrics_summary.csv
counts_dir = os.path.join(
project_dir, "qc", "cellranger_count", "2.0.0",
"refdata-cellranger-atac-GRCh38-2020-A-2.0.0", "PJB1", "outs")
mkdirs(counts_dir)
summary_file = os.path.join(counts_dir, "summary.csv")
with open(summary_file, 'w') as fp:
fp.write(ATAC_SUMMARY_2_0_0)
# Add QC info file
with open(os.path.join(project_dir, "qc", "qc.info"), 'wt') as fp:
fp.write(
"""Cellranger reference datasets\t/data/refdata-cellranger-atac-GRCh38-2020-A-2.0.0
Cellranger version\t2.0.0
""")
# Check initial cell count
print("Checking number of cells")
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, None)
# Update the cell counts
print("Updating number of cells")
set_cell_count_for_project(project_dir)
# Check updated cell count
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, 3582)
def test_set_cell_count_for_cellplex_project(self):
"""
set_cell_count_for_project: test for multiplexed data (CellPlex)
"""
# Set up mock project
project_dir = self._make_mock_analysis_project(
"10xGenomics Chromium 3'v3", "CellPlex")
# Build mock cellranger multi output directory
multi_dir = os.path.join(project_dir, "qc", "cellranger_multi",
"6.0.0",
"refdata-cellranger-gex-GRCh38-2020-A",
"outs")
mkdirs(multi_dir)
for sample in (
"PBA",
"PBB",
):
sample_dir = os.path.join(multi_dir, "per_sample_outs", sample)
mkdirs(sample_dir)
summary_file = os.path.join(sample_dir, "metrics_summary.csv")
with open(summary_file, 'wt') as fp:
fp.write(CELLPLEX_METRICS_SUMMARY)
web_summary = os.path.join(sample_dir, "web_summary.html")
with open(web_summary, 'wt') as fp:
fp.write("Placeholder for web_summary.html\n")
# Add QC info file
with open(os.path.join(project_dir, "qc", "qc.info"), 'wt') as fp:
fp.write(
"""Cellranger reference datasets\t/data/refdata-cellranger-gex-GRCh38-2020-A
Cellranger version\t6.0.0
""")
# Check initial cell count
print("Checking number of cells")
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, None)
# Update the cell counts
print("Updating number of cells")
set_cell_count_for_project(project_dir)
# Check updated cell count
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, 10350)
def test_set_cell_count_project_missing_library_type_no_subdirs(self):
"""
set_cell_count_for_project: test for scRNA-seq when library not set (old-style output)
"""
# Set up mock project with library type not set
project_dir = self._make_mock_analysis_project(
"10xGenomics Chromium 3'v3", None)
# Add metrics_summary.csv
counts_dir = os.path.join(project_dir, "qc", "cellranger_count",
"PJB1", "outs")
mkdirs(counts_dir)
metrics_summary_file = os.path.join(counts_dir, "metrics_summary.csv")
with open(metrics_summary_file, 'w') as fp:
fp.write(METRICS_SUMMARY)
# Check initial cell count
print("Checking number of cells")
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, None)
# Update the cell counts
print("Updating number of cells")
set_cell_count_for_project(project_dir)
# Check updated cell count
self.assertEqual(
AnalysisProject("PJB1", project_dir).info.number_of_cells, 2272)