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commands/make_fastqs_cmd: add unit tests for 10x protocols using Illumina indexes.
Updates the unit tests to include '10_atac', '10x_multiome_gex' and '10x_multiome_atac' Fastq generation protocols with Illumina indexes.
1 parent 981ddc7 commit f33c2ac

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Lines changed: 211 additions & 10 deletions

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‎auto_process_ngs/test/commands/test_make_fastqs_cmd.py‎

Lines changed: 211 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -481,8 +481,8 @@ def test_make_fastqs_10x_chromium_sc_protocol_illumina_indices(self):
481481
"Missing file: %s" % filen)
482482

483483
#@unittest.skip("Skipped")
484-
def test_make_fastqs_10x_atac_protocol(self):
485-
"""make_fastqs: 10x_atac protocol
484+
def test_make_fastqs_10x_atac_protocol_10x_indexes(self):
485+
"""make_fastqs: 10x_atac protocol (10x indexes)
486486
"""
487487
# Sample sheet with 10xGenomics SC ATAC-seq indices
488488
samplesheet_10x_atac_indices = """[Data]
@@ -550,6 +550,73 @@ def test_make_fastqs_10x_atac_protocol(self):
550550
os.path.join(analysis_dir,filen)),
551551
"Missing file: %s" % filen)
552552

553+
#@unittest.skip("Skipped")
554+
def test_make_fastqs_10x_atac_protocol_illumina_indexes(self):
555+
"""make_fastqs: 10x_atac protocol (Illumina indexes)
556+
"""
557+
# Sample sheet with 10xGenomics SC ATAC-seq Illumina indices
558+
samplesheet_10x_atac_indices = """[Data]
559+
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
560+
smpl1,smpl1,,,SI-NA-A1,TGTCCCAACG,10xGenomics,
561+
smpl2,smpl2,,,SI-NA-B1,AGTCCCATCA,10xGenomics,
562+
"""
563+
sample_sheet = os.path.join(self.wd,"SampleSheet.csv")
564+
with open(sample_sheet,'w') as fp:
565+
fp.write(samplesheet_10x_atac_indices)
566+
# Create mock source data
567+
illumina_run = MockIlluminaRun(
568+
"171020_NB500968_00002_AHGXXXX",
569+
"nextseq",
570+
bases_mask="y101,I8,I8,y101",
571+
top_dir=self.wd)
572+
illumina_run.create()
573+
# Create mock bcl2fastq
574+
MockBcl2fastq2Exe.create(os.path.join(self.bin,
575+
"bcl2fastq"))
576+
os.environ['PATH'] = "%s:%s" % (self.bin,
577+
os.environ['PATH'])
578+
# Do the test
579+
ap = AutoProcess(settings=self.settings)
580+
ap.setup(os.path.join(self.wd,
581+
"171020_NB500968_00002_AHGXXXX"),
582+
sample_sheet=sample_sheet)
583+
self.assertTrue(ap.params.sample_sheet is not None)
584+
self.assertEqual(ap.params.bases_mask,"auto")
585+
self.assertTrue(ap.params.primary_data_dir is None)
586+
self.assertFalse(ap.params.acquired_primary_data)
587+
make_fastqs(ap,protocol="10x_atac")
588+
# Check parameters
589+
self.assertEqual(ap.params.bases_mask,"auto")
590+
self.assertEqual(ap.params.primary_data_dir,
591+
os.path.join(self.wd,
592+
"171020_NB500968_00002_AHGXXXX_analysis",
593+
"primary_data"))
594+
self.assertTrue(ap.params.acquired_primary_data)
595+
self.assertEqual(ap.params.unaligned_dir,"bcl2fastq")
596+
self.assertEqual(ap.params.barcode_analysis_dir,"barcode_analysis")
597+
self.assertEqual(ap.params.stats_file,"statistics.info")
598+
# Check outputs
599+
analysis_dir = os.path.join(
600+
self.wd,
601+
"171020_NB500968_00002_AHGXXXX_analysis")
602+
for subdir in (os.path.join("primary_data",
603+
"171020_NB500968_00002_AHGXXXX"),
604+
os.path.join("logs",
605+
"002_make_fastqs_10x_atac"),
606+
"bcl2fastq",):
607+
self.assertTrue(os.path.isdir(
608+
os.path.join(analysis_dir,subdir)),
609+
"Missing subdir: %s" % subdir)
610+
for filen in ("statistics.info",
611+
"statistics_full.info",
612+
"per_lane_statistics.info",
613+
"per_lane_sample_stats.info",
614+
"projects.info",
615+
"processing_qc.html"):
616+
self.assertTrue(os.path.isfile(
617+
os.path.join(analysis_dir,filen)),
618+
"Missing file: %s" % filen)
619+
553620
#@unittest.skip("Skipped")
554621
def test_make_fastqs_10x_visium_protocol(self):
555622
"""make_fastqs: 10x_visium protocol
@@ -764,8 +831,8 @@ def test_make_fastqs_10x_visium_protocol_reverse_complement_workflow_B(self):
764831
"Missing file: %s" % filen)
765832

766833
#@unittest.skip("Skipped")
767-
def test_make_fastqs_10x_multiome_protocol_gex(self):
768-
"""make_fastqs: 10x_multiome protocol (GEX data)
834+
def test_make_fastqs_10x_multiome_gex_protocol_10x_indexes(self):
835+
"""make_fastqs: 10x_multiome_gex protocol (10x indexes)
769836
"""
770837
# Sample sheet with 10xGenomics indices
771838
samplesheet_10x_atac_indices = """[Data]
@@ -800,7 +867,74 @@ def test_make_fastqs_10x_multiome_protocol_gex(self):
800867
self.assertEqual(ap.params.bases_mask,"auto")
801868
self.assertTrue(ap.params.primary_data_dir is None)
802869
self.assertFalse(ap.params.acquired_primary_data)
803-
make_fastqs(ap,protocol="10x_multiome")
870+
make_fastqs(ap,protocol="10x_multiome_gex")
871+
# Check parameters
872+
self.assertEqual(ap.params.bases_mask,"auto")
873+
self.assertEqual(ap.params.primary_data_dir,
874+
os.path.join(self.wd,
875+
"171020_NB500968_00002_AHGXXXX_analysis",
876+
"primary_data"))
877+
self.assertTrue(ap.params.acquired_primary_data)
878+
self.assertEqual(ap.params.unaligned_dir,"bcl2fastq")
879+
self.assertEqual(ap.params.barcode_analysis_dir,"barcode_analysis")
880+
self.assertEqual(ap.params.stats_file,"statistics.info")
881+
# Check outputs
882+
analysis_dir = os.path.join(
883+
self.wd,
884+
"171020_NB500968_00002_AHGXXXX_analysis")
885+
for subdir in (os.path.join("primary_data",
886+
"171020_NB500968_00002_AHGXXXX"),
887+
os.path.join("logs",
888+
"002_make_fastqs_10x_multiome_gex"),
889+
"bcl2fastq",):
890+
self.assertTrue(os.path.isdir(
891+
os.path.join(analysis_dir,subdir)),
892+
"Missing subdir: %s" % subdir)
893+
for filen in ("statistics.info",
894+
"statistics_full.info",
895+
"per_lane_statistics.info",
896+
"per_lane_sample_stats.info",
897+
"projects.info",
898+
"processing_qc.html"):
899+
self.assertTrue(os.path.isfile(
900+
os.path.join(analysis_dir,filen)),
901+
"Missing file: %s" % filen)
902+
903+
#@unittest.skip("Skipped")
904+
def test_make_fastqs_10x_multiome_gex_protocol_illumina_indexes(self):
905+
"""make_fastqs: 10x_multiome_gex protocol (Illumina indexes)
906+
"""
907+
# Sample sheet with 10xGenomics indices
908+
samplesheet_10x_atac_indices = """[Data]
909+
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
910+
smpl1,smpl1,,,SI-TT-A1,TGTCCCAACG,10xGenomics,
911+
smpl2,smpl2,,,SI-TT-B1,AGTCCCATCA,10xGenomics,
912+
"""
913+
sample_sheet = os.path.join(self.wd,"SampleSheet.csv")
914+
with open(sample_sheet,'w') as fp:
915+
fp.write(samplesheet_10x_atac_indices)
916+
# Create mock source data
917+
illumina_run = MockIlluminaRun(
918+
"171020_NB500968_00002_AHGXXXX",
919+
"nextseq",
920+
bases_mask="y101,I8,I8,y101",
921+
top_dir=self.wd)
922+
illumina_run.create()
923+
# Create mock bcl2fastq
924+
MockBcl2fastq2Exe.create(os.path.join(self.bin,
925+
"bcl2fastq"))
926+
os.environ['PATH'] = "%s:%s" % (self.bin,
927+
os.environ['PATH'])
928+
# Do the test
929+
ap = AutoProcess(settings=self.settings)
930+
ap.setup(os.path.join(self.wd,
931+
"171020_NB500968_00002_AHGXXXX"),
932+
sample_sheet=sample_sheet)
933+
self.assertTrue(ap.params.sample_sheet is not None)
934+
self.assertEqual(ap.params.bases_mask,"auto")
935+
self.assertTrue(ap.params.primary_data_dir is None)
936+
self.assertFalse(ap.params.acquired_primary_data)
937+
make_fastqs(ap,protocol="10x_multiome_gex")
804938
# Check parameters
805939
self.assertEqual(ap.params.bases_mask,"auto")
806940
self.assertEqual(ap.params.primary_data_dir,
@@ -818,7 +952,7 @@ def test_make_fastqs_10x_multiome_protocol_gex(self):
818952
for subdir in (os.path.join("primary_data",
819953
"171020_NB500968_00002_AHGXXXX"),
820954
os.path.join("logs",
821-
"002_make_fastqs_10x_multiome"),
955+
"002_make_fastqs_10x_multiome_gex"),
822956
"bcl2fastq",):
823957
self.assertTrue(os.path.isdir(
824958
os.path.join(analysis_dir,subdir)),
@@ -834,8 +968,8 @@ def test_make_fastqs_10x_multiome_protocol_gex(self):
834968
"Missing file: %s" % filen)
835969

836970
#@unittest.skip("Skipped")
837-
def test_make_fastqs_10x_multiome_protocol_atac(self):
838-
"""make_fastqs: 10x_multiome protocol (ATAC data)
971+
def test_make_fastqs_10x_multiome_atac_protocol_10x_indexes(self):
972+
"""make_fastqs: 10x_multiome_atac protocol (10x indexes)
839973
"""
840974
# Sample sheet with 10xGenomics indices
841975
samplesheet_10x_atac_indices = """[Data]
@@ -870,7 +1004,74 @@ def test_make_fastqs_10x_multiome_protocol_atac(self):
8701004
self.assertEqual(ap.params.bases_mask,"auto")
8711005
self.assertTrue(ap.params.primary_data_dir is None)
8721006
self.assertFalse(ap.params.acquired_primary_data)
873-
make_fastqs(ap,protocol="10x_multiome")
1007+
make_fastqs(ap,protocol="10x_multiome_atac")
1008+
# Check parameters
1009+
self.assertEqual(ap.params.bases_mask,"auto")
1010+
self.assertEqual(ap.params.primary_data_dir,
1011+
os.path.join(self.wd,
1012+
"171020_NB500968_00002_AHGXXXX_analysis",
1013+
"primary_data"))
1014+
self.assertTrue(ap.params.acquired_primary_data)
1015+
self.assertEqual(ap.params.unaligned_dir,"bcl2fastq")
1016+
self.assertEqual(ap.params.barcode_analysis_dir,"barcode_analysis")
1017+
self.assertEqual(ap.params.stats_file,"statistics.info")
1018+
# Check outputs
1019+
analysis_dir = os.path.join(
1020+
self.wd,
1021+
"171020_NB500968_00002_AHGXXXX_analysis")
1022+
for subdir in (os.path.join("primary_data",
1023+
"171020_NB500968_00002_AHGXXXX"),
1024+
os.path.join("logs",
1025+
"002_make_fastqs_10x_multiome_atac"),
1026+
"bcl2fastq",):
1027+
self.assertTrue(os.path.isdir(
1028+
os.path.join(analysis_dir,subdir)),
1029+
"Missing subdir: %s" % subdir)
1030+
for filen in ("statistics.info",
1031+
"statistics_full.info",
1032+
"per_lane_statistics.info",
1033+
"per_lane_sample_stats.info",
1034+
"projects.info",
1035+
"processing_qc.html"):
1036+
self.assertTrue(os.path.isfile(
1037+
os.path.join(analysis_dir,filen)),
1038+
"Missing file: %s" % filen)
1039+
1040+
#@unittest.skip("Skipped")
1041+
def test_make_fastqs_10x_multiome_atac_protocol_illumina_indexes(self):
1042+
"""make_fastqs: 10x_multiome_atac protocol (Illumina indexes)
1043+
"""
1044+
# Sample sheet with 10xGenomics indices
1045+
samplesheet_10x_atac_indices = """[Data]
1046+
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1047+
smpl1,smpl1,,,SI-TT-A1,TGTCCCAACG,10xGenomics,
1048+
smpl2,smpl2,,,SI-TT-B1,AGTCCCATCA,10xGenomics,
1049+
"""
1050+
sample_sheet = os.path.join(self.wd,"SampleSheet.csv")
1051+
with open(sample_sheet,'w') as fp:
1052+
fp.write(samplesheet_10x_atac_indices)
1053+
# Create mock source data
1054+
illumina_run = MockIlluminaRun(
1055+
"171020_NB500968_00002_AHGXXXX",
1056+
"nextseq",
1057+
bases_mask="y101,I8,I8,y101",
1058+
top_dir=self.wd)
1059+
illumina_run.create()
1060+
# Create mock bcl2fastq
1061+
MockBcl2fastq2Exe.create(os.path.join(self.bin,
1062+
"bcl2fastq"))
1063+
os.environ['PATH'] = "%s:%s" % (self.bin,
1064+
os.environ['PATH'])
1065+
# Do the test
1066+
ap = AutoProcess(settings=self.settings)
1067+
ap.setup(os.path.join(self.wd,
1068+
"171020_NB500968_00002_AHGXXXX"),
1069+
sample_sheet=sample_sheet)
1070+
self.assertTrue(ap.params.sample_sheet is not None)
1071+
self.assertEqual(ap.params.bases_mask,"auto")
1072+
self.assertTrue(ap.params.primary_data_dir is None)
1073+
self.assertFalse(ap.params.acquired_primary_data)
1074+
make_fastqs(ap,protocol="10x_multiome_atac")
8741075
# Check parameters
8751076
self.assertEqual(ap.params.bases_mask,"auto")
8761077
self.assertEqual(ap.params.primary_data_dir,
@@ -888,7 +1089,7 @@ def test_make_fastqs_10x_multiome_protocol_atac(self):
8881089
for subdir in (os.path.join("primary_data",
8891090
"171020_NB500968_00002_AHGXXXX"),
8901091
os.path.join("logs",
891-
"002_make_fastqs_10x_multiome"),
1092+
"002_make_fastqs_10x_multiome_atac"),
8921093
"bcl2fastq",):
8931094
self.assertTrue(os.path.isdir(
8941095
os.path.join(analysis_dir,subdir)),

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