def test_group(self):
"""BarcodeCounter: check grouping of barcode sequences
"""
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
bc.count_barcode("GTCACGCGGTA",lane=2,incr=296201)
bc.count_barcode("GTCACGCGGTT",lane=2,incr=2853)
bc.count_barcode("GTCACGCTGTT",lane=2,incr=278539)
## 2 mismatches across all lanes
groups = bc.group(None,mismatches=2)
##"GCTGCGCGGTC","GCTGCGCGGTA","GATGCGCGGTA" = 338568
##"TATGCGCGGTA","CATGCGCGGTA" = 293834
##"GTCACGCGGTA","GTCACGCTGTT","GTCACGCGGTT" = 577593
self.assertEqual(len(groups),3)
self.assertEqual(groups[0].reference,"GTCACGCGGTA")
self.assertEqual(groups[0].sequences,["GTCACGCGGTA",
"GTCACGCTGTT",
"GTCACGCGGTT"])
self.assertEqual(groups[0].counts,577593)
self.assertEqual(groups[1].reference,"GCTGCGCGGTC")
self.assertEqual(groups[1].sequences,["GCTGCGCGGTC",
"GCTGCGCGGTA",
"GATGCGCGGTA"])
self.assertEqual(groups[1].counts,338568)
self.assertEqual(groups[2].reference,"TATGCGCGGTA")
self.assertEqual(groups[2].sequences,["TATGCGCGGTA",
"CATGCGCGGTA"])
self.assertEqual(groups[2].counts,293834)
## 1 mismatch across all lanes
groups = bc.group(None,mismatches=1)
##"TATGCGCGGTA","CATGCGCGGTA","GATGCGCGGTA" = 299155
##"GCTGCGCGGTC","GCTGCGCGGTA" = 333247
##"GTCACGCGGTA","GTCACGCGGTT" = 299054
##"GTCACGCTGTT" = 278539
self.assertEqual(len(groups),4)
self.assertEqual(groups[0].reference,"GCTGCGCGGTC")
self.assertEqual(groups[0].sequences,["GCTGCGCGGTC",
"GCTGCGCGGTA"])
self.assertEqual(groups[0].counts,333247)
self.assertEqual(groups[1].reference,"TATGCGCGGTA")
self.assertEqual(groups[1].sequences,["TATGCGCGGTA",
"CATGCGCGGTA",
"GATGCGCGGTA"])
self.assertEqual(groups[1].counts,299155)
self.assertEqual(groups[2].reference,"GTCACGCGGTA")
self.assertEqual(groups[2].sequences,["GTCACGCGGTA",
"GTCACGCGGTT"])
self.assertEqual(groups[2].counts,299054)
self.assertEqual(groups[3].reference,"GTCACGCTGTT")
self.assertEqual(groups[3].sequences,["GTCACGCTGTT",])
self.assertEqual(groups[3].counts,278539)
## 1 mismatch in lane 1
groups = bc.group(1,mismatches=1)
##"TATGCGCGGTA","CATGCGCGGTA","GATGCGCGGTA" = 299155
##"GCTGCGCGGTC","GCTGCGCGGTA" = 333247
self.assertEqual(len(groups),2)
self.assertEqual(groups[0].reference,"GCTGCGCGGTC")
self.assertEqual(groups[0].sequences,["GCTGCGCGGTC",
"GCTGCGCGGTA"])
self.assertEqual(groups[0].counts,333247)
self.assertEqual(groups[1].reference,"TATGCGCGGTA")
self.assertEqual(groups[1].sequences,["TATGCGCGGTA",
"CATGCGCGGTA",
"GATGCGCGGTA"])
self.assertEqual(groups[1].counts,299155)
## 2 mismatches across all lanes
groups = bc.group(None,mismatches=2)
##"GCTGCGCGGTC","GCTGCGCGGTA","GATGCGCGGTA" = 338568
##"TATGCGCGGTA","CATGCGCGGTA" = 293834
##"GTCACGCGGTA","GTCACGCTGTT","GTCACGCGGTT" = 577593
self.assertEqual(len(groups),3)
self.assertEqual(groups[0].reference,"GTCACGCGGTA")
self.assertEqual(groups[0].sequences,["GTCACGCGGTA",
"GTCACGCTGTT",
"GTCACGCGGTT"])
self.assertEqual(groups[0].counts,577593)
self.assertEqual(groups[1].reference,"GCTGCGCGGTC")
self.assertEqual(groups[1].sequences,["GCTGCGCGGTC",
"GCTGCGCGGTA",
"GATGCGCGGTA"])
self.assertEqual(groups[1].counts,338568)
self.assertEqual(groups[2].reference,"TATGCGCGGTA")
self.assertEqual(groups[2].sequences,["TATGCGCGGTA",
"CATGCGCGGTA"])
self.assertEqual(groups[2].counts,293834)
def test_group(self):
"""BarcodeCounter: check grouping of barcode sequences
"""
bc = BarcodeCounter()
bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
bc.count_barcode("GTCACGCGGTA",lane=2,incr=296201)
bc.count_barcode("GTCACGCGGTT",lane=2,incr=2853)
bc.count_barcode("GTCACGCTGTT",lane=2,incr=278539)
## 2 mismatches across all lanes
groups = bc.group(None,mismatches=2)
##"GCTGCGCGGTC","GCTGCGCGGTA","GATGCGCGGTA" = 338568
##"TATGCGCGGTA","CATGCGCGGTA" = 293834
##"GTCACGCGGTA","GTCACGCTGTT","GTCACGCGGTT" = 577593
self.assertEqual(len(groups),3)
self.assertEqual(groups[0].reference,"GTCACGCGGTA")
self.assertEqual(groups[0].sequences,["GTCACGCGGTA",
"GTCACGCTGTT",
"GTCACGCGGTT"])
self.assertEqual(groups[0].counts,577593)
self.assertEqual(groups[1].reference,"GCTGCGCGGTC")
self.assertEqual(groups[1].sequences,["GCTGCGCGGTC",
"GCTGCGCGGTA",
"GATGCGCGGTA"])
self.assertEqual(groups[1].counts,338568)
self.assertEqual(groups[2].reference,"TATGCGCGGTA")
self.assertEqual(groups[2].sequences,["TATGCGCGGTA",
"CATGCGCGGTA"])
self.assertEqual(groups[2].counts,293834)
## 1 mismatch across all lanes
groups = bc.group(None,mismatches=1)
##"TATGCGCGGTA","CATGCGCGGTA","GATGCGCGGTA" = 299155
##"GCTGCGCGGTC","GCTGCGCGGTA" = 333247
##"GTCACGCGGTA","GTCACGCGGTT" = 299054
##"GTCACGCTGTT" = 278539
self.assertEqual(len(groups),4)
self.assertEqual(groups[0].reference,"GCTGCGCGGTC")
self.assertEqual(groups[0].sequences,["GCTGCGCGGTC",
"GCTGCGCGGTA"])
self.assertEqual(groups[0].counts,333247)
self.assertEqual(groups[1].reference,"TATGCGCGGTA")
self.assertEqual(groups[1].sequences,["TATGCGCGGTA",
"CATGCGCGGTA",
"GATGCGCGGTA"])
self.assertEqual(groups[1].counts,299155)
self.assertEqual(groups[2].reference,"GTCACGCGGTA")
self.assertEqual(groups[2].sequences,["GTCACGCGGTA",
"GTCACGCGGTT"])
self.assertEqual(groups[2].counts,299054)
self.assertEqual(groups[3].reference,"GTCACGCTGTT")
self.assertEqual(groups[3].sequences,["GTCACGCTGTT",])
self.assertEqual(groups[3].counts,278539)
## 1 mismatch in lane 1
groups = bc.group(1,mismatches=1)
##"TATGCGCGGTA","CATGCGCGGTA","GATGCGCGGTA" = 299155
##"GCTGCGCGGTC","GCTGCGCGGTA" = 333247
self.assertEqual(len(groups),2)
self.assertEqual(groups[0].reference,"GCTGCGCGGTC")
self.assertEqual(groups[0].sequences,["GCTGCGCGGTC",
"GCTGCGCGGTA"])
self.assertEqual(groups[0].counts,333247)
self.assertEqual(groups[1].reference,"TATGCGCGGTA")
self.assertEqual(groups[1].sequences,["TATGCGCGGTA",
"CATGCGCGGTA",
"GATGCGCGGTA"])
self.assertEqual(groups[1].counts,299155)
## 2 mismatches across all lanes
groups = bc.group(None,mismatches=2)
##"GCTGCGCGGTC","GCTGCGCGGTA","GATGCGCGGTA" = 338568
##"TATGCGCGGTA","CATGCGCGGTA" = 293834
##"GTCACGCGGTA","GTCACGCTGTT","GTCACGCGGTT" = 577593
self.assertEqual(len(groups),3)
self.assertEqual(groups[0].reference,"GTCACGCGGTA")
self.assertEqual(groups[0].sequences,["GTCACGCGGTA",
"GTCACGCTGTT",
"GTCACGCGGTT"])
self.assertEqual(groups[0].counts,577593)
self.assertEqual(groups[1].reference,"GCTGCGCGGTC")
self.assertEqual(groups[1].sequences,["GCTGCGCGGTC",
"GCTGCGCGGTA",
"GATGCGCGGTA"])
self.assertEqual(groups[1].counts,338568)
self.assertEqual(groups[2].reference,"TATGCGCGGTA")
self.assertEqual(groups[2].sequences,["TATGCGCGGTA",
"CATGCGCGGTA"])
self.assertEqual(groups[2].counts,293834)
