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)