def test_analyse_barcodes_with_bcl2fastq_dir_and_bad_samplesheet(self):
"""
AnalyseBarcodes: raise exception for bcl2fastq directory as input using 'bad' samplesheet
"""
# Make a mock bcl2fastq output directory
datadir = MockIlluminaData(os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9"),
"bcl2fastq2",
unaligned_dir="bcl2fastq",
paired_end=True)
datadir.add_fastq_batch("AB", "AB1", "AB1_S1")
datadir.add_fastq_batch("AB", "AB2", "AB2_S2")
datadir.add_fastq_batch("CDE", "CDE3", "CDE3_S3")
datadir.add_fastq_batch("CDE", "CDE4", "CDE4_S4")
datadir.add_fastq_batch("", "Undetermined", "Undetermined_S0")
datadir.create()
# Add data to Fastq files
self._insert_fastq_reads(
os.path.join(self.wd, "200428_M00879_0087_000000000-AGEW9"))
# Create "bad" sample sheet with mixture of empty and
# non-empty indices in a lane
sample_sheet = os.path.join(self.wd, "custom_SampleSheet.csv")
with open(sample_sheet, 'w') as fp:
fp.write("""[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
AB1,AB1,,,D701,CGTGTAGG,D501,GACCTGAA,AB,
AB2,AB2,,,D702,CGTGTAGG,D501,ATGTAACT,AB,
CDE3,CDE3,,,,,,,CDE,
CDE4,CDE4,,,,,,,CDE,
""")
# Set up and run pipeline
p = AnalyseBarcodes(bcl2fastq_dir=os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9", "bcl2fastq"))
self.assertRaises(Exception,
AnalyseBarcodes.run,
os.path.join(self.wd, "barcode_analysis"),
sample_sheet=sample_sheet,
working_dir=self.wd,
poll_interval=POLL_INTERVAL)
def test_analyse_barcodes_with_bcl2fastq_dir_no_samplesheet(self):
"""
AnalyseBarcodes: bcl2fastq directory as input (no samplesheet)
"""
# Make a mock bcl2fastq output directory
datadir = MockIlluminaData(os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9"),
"bcl2fastq2",
unaligned_dir="bcl2fastq",
paired_end=True)
datadir.add_fastq_batch("AB", "AB1", "AB1_S1")
datadir.add_fastq_batch("AB", "AB2", "AB2_S2")
datadir.add_fastq_batch("CDE", "CDE3", "CDE3_S3")
datadir.add_fastq_batch("CDE", "CDE4", "CDE4_S4")
datadir.add_fastq_batch("", "Undetermined", "Undetermined_S0")
datadir.create()
# Add data to Fastq files
self._insert_fastq_reads(
os.path.join(self.wd, "200428_M00879_0087_000000000-AGEW9"))
# Set up and run pipeline
p = AnalyseBarcodes(bcl2fastq_dir=os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9", "bcl2fastq"))
exit_code = p.run(os.path.join(self.wd, "barcode_analysis"),
working_dir=self.wd,
poll_interval=POLL_INTERVAL)
# Check outputs
self.assertEqual(exit_code, 0)
self.assertTrue(
os.path.isdir(os.path.join(self.wd, "barcode_analysis")),
"Missing dir: barcode_analysis")
self.assertTrue(
os.path.isdir(os.path.join(self.wd, "barcode_analysis", "counts")),
"Missing dir: barcode_analysis/counts")
for f in (
"AB.AB1_S1_L001_R1_001.fastq.gz.counts",
"AB.AB2_S2_L001_R1_001.fastq.gz.counts",
"CDE.CDE3_S3_L001_R1_001.fastq.gz.counts",
"CDE.CDE4_S4_L001_R1_001.fastq.gz.counts",
"__undetermined__.Undetermined_S0_L001_R1_001.fastq.gz.counts"
):
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "counts", f)),
"Missing file: %s" % f)
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.report")),
"Missing file: barcodes.report")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.xls")),
"Missing file: barcodes.xls")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.html")),
"Missing file: barcodes.html")
# Check that the report content is non-trivial
barcodes_report = os.path.join(self.wd, "barcode_analysis",
"barcodes.report")
with open(barcodes_report, 'rt') as fp:
contents = fp.read()
self.assertTrue("Barcode analysis for lane #1" in contents)
self.assertTrue(
"#Rank\tIndex\tSample\tN_seqs\tN_reads\t%reads\t(%Total_reads)"
in contents)
# Expect 12 lines of content in total
self.assertEqual(contents.count('\n'), 12)
def test_analyse_barcodes_with_multi_lane_samplesheet(self):
"""
AnalyseBarcodes: multi-lane sample sheet as input
"""
# Create sample sheet
sample_sheet = os.path.join(self.wd, "custom_SampleSheet.csv")
with open(sample_sheet, 'w') as fp:
fp.write("""[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
1,AB1,AB1,,,D701,CGTGTAGG,D501,GACCTGAA,AB,
1,AB2,AB2,,,D702,CGTGTAGG,D501,ATGTAACT,AB,
2,CDE3,CDE3,,,D701,GACCTGAA,D501,CGTGTAGG,CDE,
2,CDE4,CDE4,,,D702,ATGTAACT,D501,CGTGTAGG,CDE,
""")
# Set up pipeline before bcl2fastq directory exists
p = AnalyseBarcodes(sample_sheet=sample_sheet)
# Create the bcl2fastq directory before running pipeline
datadir = MockIlluminaData(os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9"),
"bcl2fastq2",
unaligned_dir="bcl2fastq",
paired_end=True)
datadir.add_fastq_batch("AB", "AB1", "AB1_S1", lanes=(1, ))
datadir.add_fastq_batch("AB", "AB2", "AB2_S2", lanes=(1, ))
datadir.add_fastq_batch("CDE", "CDE3", "CDE3_S3", lanes=(2, ))
datadir.add_fastq_batch("CDE", "CDE4", "CDE4_S4", lanes=(2, ))
datadir.add_fastq_batch("",
"Undetermined",
"Undetermined_S0",
lanes=(1, 2))
datadir.create()
# Add data to Fastq files
self._insert_fastq_reads(
os.path.join(self.wd, "200428_M00879_0087_000000000-AGEW9"))
# Run the pipeline
exit_code = p.run(os.path.join(self.wd, "barcode_analysis"),
bcl2fastq_dir=os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9",
"bcl2fastq"),
working_dir=self.wd,
poll_interval=POLL_INTERVAL)
# Check outputs
self.assertEqual(exit_code, 0)
self.assertTrue(
os.path.isdir(os.path.join(self.wd, "barcode_analysis")),
"Missing dir: barcode_analysis")
self.assertTrue(
os.path.isdir(os.path.join(self.wd, "barcode_analysis", "counts")),
"Missing dir: barcode_analysis/counts")
for f in (
"AB.AB1_S1_L001_R1_001.fastq.gz.counts",
"AB.AB2_S2_L001_R1_001.fastq.gz.counts",
"CDE.CDE3_S3_L002_R1_001.fastq.gz.counts",
"CDE.CDE4_S4_L002_R1_001.fastq.gz.counts",
"__undetermined__.Undetermined_S0_L001_R1_001.fastq.gz.counts"
):
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "counts", f)),
"Missing file: %s" % f)
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.report")),
"Missing file: barcodes.report")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.xls")),
"Missing file: barcodes.xls")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.html")),
"Missing file: barcodes.html")
# Check that the report content is non-trivial
barcodes_report = os.path.join(self.wd, "barcode_analysis",
"barcodes.report")
with open(barcodes_report, 'rt') as fp:
contents = fp.read()
self.assertTrue("Barcode analysis for lane #1" in contents)
self.assertTrue("Barcode analysis for lane #2" in contents)
self.assertTrue(
"#Rank\tIndex\tSample\tN_seqs\tN_reads\t%reads\t(%Total_reads)"
in contents)
self.assertTrue(
"Problems detected:\n * Underrepresented samples" in contents)
self.assertTrue(
" 1\tTCCTGA\t\t1\t2\t100.0%\t(100.0%)" in contents)
self.assertTrue(
"The following samples are underrepresented:" in contents)
for line in (
"AB1\tCGTGTAGG+GACCTGAA\t\t<0.1%",
"AB2\tCGTGTAGG+ATGTAACT\t\t<0.1%",
"CDE3\tGACCTGAA+CGTGTAGG\t\t<0.1%",
"CDE4\tATGTAACT+CGTGTAGG\t\t<0.1%",
):
self.assertTrue(line in contents)
# Expect at least 12 lines of content in total
self.assertTrue(contents.count('\n') >= 12)
def test_analyse_barcodes_with_samplesheet_and_10x_indices(self):
"""
AnalyseBarcodes: sample sheet with 10xGenomics indices
"""
# Create sample sheet
sample_sheet = os.path.join(self.wd, "custom_SampleSheet.csv")
with open(sample_sheet, 'w') as fp:
fp.write("""[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
AB1,AB1,,,D501,SI-GA-A2,AB,
AB2,AB2,,,D501,SI-GA-B2,AB,
CDE3,CDE3,,,D501,SI-GA-C2,CDE,
CDE4,CDE4,,,D501,SI-GA-D2,CDE,
""")
# Set up pipeline before bcl2fastq directory exists
p = AnalyseBarcodes(sample_sheet=sample_sheet)
# Create the bcl2fastq directory before running pipeline
datadir = MockIlluminaData(os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9"),
"bcl2fastq2",
unaligned_dir="bcl2fastq",
paired_end=True)
datadir.add_fastq_batch("AB", "AB1", "AB1_S1")
datadir.add_fastq_batch("AB", "AB2", "AB2_S2")
datadir.add_fastq_batch("CDE", "CDE3", "CDE3_S3")
datadir.add_fastq_batch("CDE", "CDE4", "CDE4_S4")
datadir.add_fastq_batch("", "Undetermined", "Undetermined_S0")
datadir.create()
# Add data to Fastq files
self._insert_fastq_reads(
os.path.join(self.wd, "200428_M00879_0087_000000000-AGEW9"))
# Run the pipeline
exit_code = p.run(os.path.join(self.wd, "barcode_analysis"),
bcl2fastq_dir=os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9",
"bcl2fastq"),
working_dir=self.wd,
poll_interval=POLL_INTERVAL)
# Check outputs
self.assertEqual(exit_code, 0)
self.assertTrue(
os.path.isdir(os.path.join(self.wd, "barcode_analysis")),
"Missing dir: barcode_analysis")
self.assertTrue(
os.path.isdir(os.path.join(self.wd, "barcode_analysis", "counts")),
"Missing dir: barcode_analysis/counts")
for f in (
"AB.AB1_S1_L001_R1_001.fastq.gz.counts",
"AB.AB2_S2_L001_R1_001.fastq.gz.counts",
"CDE.CDE3_S3_L001_R1_001.fastq.gz.counts",
"CDE.CDE4_S4_L001_R1_001.fastq.gz.counts",
"__undetermined__.Undetermined_S0_L001_R1_001.fastq.gz.counts"
):
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "counts", f)),
"Missing file: %s" % f)
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.report")),
"Missing file: barcodes.report")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.xls")),
"Missing file: barcodes.xls")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.html")),
"Missing file: barcodes.html")
# Check that the report content is non-trivial
barcodes_report = os.path.join(self.wd, "barcode_analysis",
"barcodes.report")
with open(barcodes_report, 'rt') as fp:
contents = fp.read()
self.assertTrue("Barcode analysis for lane #1" in contents)
self.assertTrue(
"#Rank\tIndex\tSample\tN_seqs\tN_reads\t%reads\t(%Total_reads)"
in contents)
# Expect 12 lines of content in total
self.assertEqual(contents.count('\n'), 12)
def test_analyse_barcodes_with_bcl2fastq_dir_and_samplesheet_empty_index(
self):
"""
AnalyseBarcodes: bcl2fastq directory as input (with samplesheet, empty index)
"""
# Make a mock bcl2fastq output directory
datadir = MockIlluminaData(os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9"),
"bcl2fastq2",
unaligned_dir="bcl2fastq",
paired_end=True)
datadir.add_fastq_batch("AB", "AB1", "AB1_S1")
datadir.create()
# Add data to Fastq files
self._insert_fastq_reads(
os.path.join(self.wd, "200428_M00879_0087_000000000-AGEW9"))
# Create sample sheet with single empty index
sample_sheet = os.path.join(self.wd, "custom_SampleSheet.csv")
with open(sample_sheet, 'w') as fp:
fp.write("""[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
AB1,AB1,,,,,,,AB,
""")
# Set up and run pipeline
p = AnalyseBarcodes(bcl2fastq_dir=os.path.join(
self.wd, "200428_M00879_0087_000000000-AGEW9", "bcl2fastq"))
exit_code = p.run(os.path.join(self.wd, "barcode_analysis"),
sample_sheet=sample_sheet,
working_dir=self.wd,
poll_interval=POLL_INTERVAL)
# Check outputs
self.assertEqual(exit_code, 0)
self.assertTrue(
os.path.isdir(os.path.join(self.wd, "barcode_analysis")),
"Missing dir: barcode_analysis")
self.assertTrue(
os.path.isdir(os.path.join(self.wd, "barcode_analysis", "counts")),
"Missing dir: barcode_analysis/counts")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "counts",
"AB.AB1_S1_L001_R1_001.fastq.gz.counts")),
"Missing file: AB.AB1_S1_L001_R1_001.fastq.gz.counts")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.report")),
"Missing file: barcodes.report")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.xls")),
"Missing file: barcodes.xls")
self.assertTrue(
os.path.isfile(
os.path.join(self.wd, "barcode_analysis", "barcodes.html")),
"Missing file: barcodes.html")
# Check that the report content is non-trivial
barcodes_report = os.path.join(self.wd, "barcode_analysis",
"barcodes.report")
with open(barcodes_report, 'rt') as fp:
contents = fp.read()
self.assertTrue("Barcode analysis for lane #1" in contents)
self.assertTrue(
"#Rank\tIndex\tSample\tN_seqs\tN_reads\t%reads\t(%Total_reads)"
in contents)
self.assertTrue(
"Problems detected:\n * Underrepresented samples" in contents)
self.assertTrue(
" 1\tTCCTGA\t\t1\t1\t100.0%\t(100.0%)" in contents)
self.assertTrue(
"The following samples are underrepresented:" in contents)
self.assertTrue("AB1\t\t\t<0.1%" in contents)
# Expect at least 12 lines of content in total
self.assertTrue(contents.count('\n') >= 12)
