def test_sample_sheet_with_no_barcodes(self):
self.sample_sheet_with_no_barcodes = u"""[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
1,AB1,AB1,,,,,,,Andrew_Bloggs,
"""
linter = SampleSheetLinter(
fp=StringIO(self.sample_sheet_with_no_barcodes))
self.assertEqual(linter.has_invalid_barcodes(), list())
def test_sample_sheet_with_valid_barcodes(self):
self.sample_sheet_with_valid_barcodes = u"""[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
1,AB1,AB1,,,N701,CGATGTAT,N501,TCTTTCCC,Andrew_Bloggs,
1,AB2,AB2,,,N702,TGACCAAT,N502,TCTTTCCC,Andrew_Bloggs,
2,CD1,CD1,,,N701,CGATGTAT,N501,TCTTTCCC,Carl_Dewey,
2,FG2,FG2,,,N702,TGACCAAT,N502,TCTTTCCC,Filipe_Greer,
"""
linter = SampleSheetLinter(
fp=StringIO(self.sample_sheet_with_valid_barcodes))
self.assertEqual(linter.has_invalid_barcodes(), list())
def test_sample_sheet_with_invalid_barcodes(self):
self.sample_sheet_with_invalid_barcodes = u"""[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
1,AB1,AB1,,,N701,CGATGTNN,N501,TCTTTCCC,Andrew_Bloggs,
1,AB2,AB2,,,N702,TGACCAAT,N502,TCTTNNNN,Andrew_Bloggs,
2,CD1,CD1,,,N701,CGATGTAT,N501,TCTTTCCC,Carl_Dewey,
2,FG2,FG2,,,N702,tgaccaat,N502,tctttccc,Filipe_Greer,
3,HJ1,HJ1,,,N702,AGHJATTC,N502,TCTTTCCC,Hugh_Jaxman,
3,HJ2,HJ2,,,N702,CGATGTAT,N502,TCTTKCCC,Hugh_Jaxman,
4,KL1,KL1,,,N702,TGACC&^&,N502,TCTTTCCC,Karl_Landseer,
4,KL2,KL2,,,N702,TGACCAAT,N502,TC%$TCCC,Karl_Landseer,
"""
linter = SampleSheetLinter(
fp=StringIO(self.sample_sheet_with_invalid_barcodes))
self.assertTrue(linter.has_invalid_barcodes())
def test_sample_sheet_with_10xgenomics_barcodes(self):
self.sample_sheet_with_10xgenomics_barcodes = u"""[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1,AB1,AB1,,,N701,SI-GA-B3,Philip_Crook,
2,AB2,AB2,,,N701,SI-GA-B3,Philip_Crook,
3,AB3,AB3,,,N701,SI-GA-G1,Philip_Crook,
4,AB4,AB4,,,N701,SI-GA-G1,Philip_Crook,
5,AB5,AB5,,,N701,SI-GA-H1,Philip_Crook,
6,AB6,AB6,,,N701,SI-GA-H1,Philip_Crook,
7,AB7,AB7,,,N701,SI-P03-C9,Philip_Crook,
8,AB8,AB8,,,N701,SI-P03-C9,Philip_Crook,
"""
linter = SampleSheetLinter(
fp=StringIO(self.sample_sheet_with_10xgenomics_barcodes))
self.assertEqual(linter.has_invalid_barcodes(), list())
