def test_get_bases_mask_dual_index_no_sample_sheet(self):
"""get_bases_mask: handle dual index (no samplesheet)
"""
# Make a RunInfo.xml file
run_info_xml = os.path.join(self.wd,"RunInfo.xml")
with open(run_info_xml,'w') as fp:
fp.write(RunInfoXml.hiseq("171020_SN7001250_00002_AHGXXXX"))
# Check the bases mask
self.assertEqual(get_bases_mask(run_info_xml),"y101,I8,I8,y101")
def test_get_bases_mask_single_index_no_sample_sheet(self):
"""get_bases_mask: handle single index (no samplesheet)
"""
# Make a single index RunInfo.xml file
run_info_xml = os.path.join(self.wd,"RunInfo.xml")
with open(run_info_xml,'w') as fp:
fp.write(RunInfoXml.nextseq("171020_NB500968_00002_AHGXXXX"))
# Check the bases mask
self.assertEqual(get_bases_mask(run_info_xml),"y76,I6,y76")
def test_get_bases_mask_10x_atac_I16_I16_dual_indexes(self):
"""get_bases_mask_10x_atac: run with I16,I16 dual indexes
"""
# Make a single index RunInfo.xml file
run_info_xml = os.path.join(self.wd,"RunInfo.xml")
with open(run_info_xml,'w') as fp:
fp.write(RunInfoXml.create("171020_NB500968_00002_AHGXXXX",
"y76,I16,I16,y76",4,12))
self.assertEqual(get_bases_mask_10x_atac(run_info_xml),
"y76,I8nnnnnnnn,y16,y76")
def test_get_bases_mask_10x_atac_too_short_index(self):
"""get_bases_mask_10x_atac: run with too-short index
"""
# Make a single index RunInfo.xml file
run_info_xml = os.path.join(self.wd, "RunInfo.xml")
with open(run_info_xml, 'w') as fp:
fp.write(
RunInfoXml.create("171020_NB500968_00002_AHGXXXX",
"y76,I6,I16,y76", 4, 12))
self.assertRaises(Exception, get_bases_mask_10x_atac, run_info_xml)
def test_get_bases_mask_10x_atac_wrong_number_of_reads(self):
"""get_bases_mask_10x_atac: run with wrong number of reads
"""
# Make a single index RunInfo.xml file
run_info_xml = os.path.join(self.wd,"RunInfo.xml")
with open(run_info_xml,'w') as fp:
fp.write(RunInfoXml.create("171020_NB500968_00002_AHGXXXX",
"y76,I8,y76",4,12))
self.assertRaises(Exception,
get_bases_mask_10x_atac,
run_info_xml)
def test_get_bases_mask_dual_index_no_barcode(self):
"""get_bases_mask: handle dual index with no barcode
"""
# Make a RunInfo.xml file
run_info_xml = os.path.join(self.wd,"RunInfo.xml")
with open(run_info_xml,'w') as fp:
fp.write(RunInfoXml.hiseq("171020_SN7001250_00002_AHGXXXX"))
# Make a matching sample sheet
sample_sheet_content = """[Header]
IEMFileVersion,4
Date,11/23/2015
Workflow,GenerateFASTQ
Application,FASTQ Only
Assay,TruSeq HT
Description,
Chemistry,Amplicon
[Reads]
76
76
[Settings]
ReverseComplement,0
Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index,index2,Sample_Project,Description
1,AB1,AB1,,,,,,,AB,
2,AB2,AB2,,,,,,,AB,
3,AB1,AB1,,,,,,,AB,
4,AB2,AB2,,,,,,,AB,
5,CD1,CD1,,,,,,,CD,
6,CD2,CD2,,,,,,,CD,
7,CD1,CD1,,,,,,,CD,
8,CD2,CD2,,,,,,,CD,
"""
sample_sheet = os.path.join(self.wd,"SampleSheet.csv")
with open(sample_sheet,'w') as fp:
fp.write(sample_sheet_content)
# Check the bases mask
self.assertEqual(get_bases_mask(run_info_xml,sample_sheet),
"y101,nnnnnnnn,nnnnnnnn,y101")
def test_get_bases_mask_10xgenomics_sample_set(self):
"""get_bases_mask: handle 10xGenomics sample set IDs
"""
# Make a RunInfo.xml file
run_info_xml = os.path.join(self.wd,"RunInfo.xml")
with open(run_info_xml,'w') as fp:
fp.write(RunInfoXml.nextseq("171020_NB500968_00002_AHGXXXX"))
# Make a matching sample sheet
sample_sheet_content = """[Header]
IEMFileVersion,4
Date,4/24/2018
Workflow,GenerateFASTQ
Application,NextSeq FASTQ Only
Assay,Nextera XT v2 Set A
Description,
Chemistry,Default
[Reads]
76
76
[Settings]
Adapter,CTGTCTCTTATACACATCT
[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
SL1,SL1,,,N701,SI-GA-A2,SL,
SL2,SL2,,,N702,SI-GA-B2,SL,
SL3,SL3,,,N703,SI-GA-C2,SL,
SL4,SL4,,,N704,SI-GA-D2,SL,
"""
sample_sheet = os.path.join(self.wd,"SampleSheet.csv")
with open(sample_sheet,'w') as fp:
fp.write(sample_sheet_content)
# Check the bases mask
self.assertEqual(get_bases_mask(run_info_xml,sample_sheet),
"y76,I6,y76")
def test_get_bases_mask_single_index_truncated(self):
"""get_bases_mask: handle truncated single index
"""
# Make a single index RunInfo.xml file
run_info_xml = os.path.join(self.wd,"RunInfo.xml")
with open(run_info_xml,'w') as fp:
fp.write(RunInfoXml.nextseq("171020_NB500968_00002_AHGXXXX"))
# Make a matching sample sheet
sample_sheet_content = """[Header]
IEMFileVersion,4
Date,11/23/2015
Workflow,GenerateFASTQ
Application,FASTQ Only
Assay,TruSeq HT
Description,
Chemistry,Amplicon
[Reads]
76
76
[Settings]
ReverseComplement,0
Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
AB1,AB1,,,D701,CGTGT,AB,
AB2,AB2,,,D702,ATTCA,AB,
"""
sample_sheet = os.path.join(self.wd,"SampleSheet.csv")
with open(sample_sheet,'w') as fp:
fp.write(sample_sheet_content)
# Check the bases mask
self.assertEqual(get_bases_mask(run_info_xml,sample_sheet),
"y76,I5n,y76")