def test_parse_productive_clone(self):
clone = sequenta.sequenta_parseline(self.productive, self.index2column)
self.assertTrue(clone is not None)
self.assertEqual(clone.count, 16967)
self.assertEqual(clone.freq, 10**(-1.880))
vgenes = ["TRBV7-9"]
self.assertTrue(set(clone.vgenes) == set(vgenes))
valleles = ["TRBV7-9*01", "TRBV7-9*02", "TRBV7-9*03"]
self.assertTrue(set(clone.valleles) == set(valleles))
jgenes = ["TRBJ2-7"]
self.assertTrue(set(clone.jgenes) == set(jgenes))
jalleles = ["TRBJ2-7*01"]
self.assertTrue(set(clone.jalleles) == set(jalleles))
dalleles = ["TRBD2*01", "TRBD2*02"]
self.assertTrue(set(clone.dalleles) == set(dalleles))
dgenes = ["TRBD2"]
self.assertTrue(set(clone.dgenes) == set(dgenes))
self.assertTrue(clone.productive)
nuc = ("GGGGACTCGGCCATGTATCTCTGTGCCAGCAGCTCAGGGACTAGCGCTTCCTACGAGCAGT"
+ "ACTTCGGGCCGGGCACCAGGCTCACGGTCACA")
self.assertEqual(clone.nuc, nuc)
cdr3nuc = "TGTGCCAGCAGCTCAGGGACTAGCGCTTCCTACGAGCAGTACTTC"
self.assertEqual(clone.cdr3nuc, cdr3nuc)
aa = "GDSAMYLCASSSGTSASYEQYFGPGTRLTVT"
self.assertEqual(clone.aa, aa)
cdr3aa = "CASSSGTSASYEQYF"
self.assertEqual(clone.cdr3aa, cdr3aa)
lastvpos = 35 - 2
self.assertEqual(clone.lastvpos, lastvpos)
def test_parse_minfield_clone(self):
clonestr = ("16967\t-1.880\tTGTGCCAGCAGCTTAGGGGAAAACATTCAGTACTTC\t"
+ "TRBV13\tTRBJ2-4")
index2column = {1: 'Log10_Frequency', 0: 'Total_Read_Count',
2: 'Clone_Sequence', 3: 'V_Segment_Major_Gene',
4: 'J_Segment_Major_Gene'}
clone = sequenta.sequenta_parseline(clonestr, index2column)
self.assertTrue(clone is not None)
def test_parse_water_clone(self):
water = ("RNA_TCB_H2O_Micro_20130121_PCR289_Run047\tRun047_6"
+ "H2O_Micro_20130121_PCR289\tWater\t5\t"
+ "-1.754\t9\t32.95\t88.89\tTRBJ2-5\tTRBJ2-5*01"
+ "43.00\t4.000\tTRBV15\tTRBV15\tTRBV15*02\t"
+ "34.00\t.0\t17.00\t15.00\t9\t3\t"
+ "TRBD2*02\t5\ttrue\tGAGCACCAGGAGCCGCGTGCC"
+ "TGGCCCGAAGTACTGGGTCTCTCGCTCTCGACCCTCTCTGCTGGTGGCACAC"
+ "AGGTACATGGCTGCGTCCCCC\t\tTGTGCCACCAGCAGAGAGGGT"
+ "CGAGAGCGAGAGACCCAGTACTTC\tGDAAMYLCATSREGRERETQY"
+ "FGPGTRLLVL\n")
clone = sequenta.sequenta_parseline(water, self.index2column)
self.assertTrue(clone is None)
