def test_reformat_read(self):
"""
Tests basic reformatting of read to output known correct result
"""
barcodes = {"GTTG" : "R01"}
name = "@M01356\n"
seq = "CCGGTTGTATTTCATTCTGCCCAGAGCAAAATACATGTGACAAAA\n"
plus = "+\n"
quality = "BBBBCBCFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHH\n"
barcode, randomer, read = reformat_read(name, seq, plus, quality, barcodes)
self.assertEqual("GTTG", barcode)
self.assertEqual("CCGGTTGTA", randomer)
self.assertEqual("@CCGGTTGTA:M01356\nTTTCATTCTGCCCAGAGCAAAATACATGTGACAAAA\n+\nFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHH\n", read)
def test_variable_length_barcodes(self):
"""
Lets see if a length 6 barcode works
"""
barcodes = {"GTTTTG" : "R01"}
name = "@M01356\n"
seq = "CCGGTTTTGTATTTCATTCTGCCCAGAGCAAAATACATGTGACAAAA\n"
plus = "+\n"
quality = "FFBBBBCBCFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHH\n"
barcode, randomer, read = reformat_read(name, seq, plus, quality, barcodes)
self.assertEqual("GTTTTG", barcode)
self.assertEqual("CCGGTTTTGTA", randomer)
self.assertEqual("@CCGGTTTTGTA:M01356\nTTTCATTCTGCCCAGAGCAAAATACATGTGACAAAA\n+\nFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHH\n", read)
def test_multiple_barcodes(self):
"""
Tests if a length 4 and 6 barcode can play together
"""
barcodes = {"GTTG" : "R00",
"GTTTTG" : "R01"}
name = "@M01356\n"
seq = "CCGGTTTTGTATTTCATTCTGCCCAGAGCAAAATACATGTGACAAAA\n"
plus = "+\n"
quality = "FFBBBBCBCFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHH\n"
barcode, randomer, read = reformat_read(name, seq, plus, quality, barcodes)
self.assertEqual("GTTTTG", barcode)
self.assertEqual("CCGGTTTTGTA", randomer)
self.assertEqual("@CCGGTTTTGTA:M01356\nTTTCATTCTGCCCAGAGCAAAATACATGTGACAAAA\n+\nFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHH\n", read)
