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| import unittest | |
| import sys | |
| from fatool import Sequence | |
| from string import maketrans | |
| class TestSequence(unittest.TestCase): | |
| def setUp(self): | |
| pass | |
| def test_setUpSequence(self): | |
| c = Sequence('>name', 'ACTGactg') | |
| self.assertTrue( isinstance(c, Sequence) ) | |
| self.assertEqual(c.name, '>name') | |
| self.assertEqual(c.seq, 'ACTGactg') | |
| def test_contig_str(self): | |
| c = Sequence('>name', 'ACTGactg') | |
| self.assertEqual(str(c), '>name\nACTGactg\n') | |
| def test_validate_name_string(self): | |
| c = Sequence('>name', 'ACTGactg') | |
| self.assertEqual(c.validate_name_string('>name'), 1) | |
| def test_generic_validation(self): | |
| self.assertEqual(Sequence.generic_validate('ACTGactg', '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 1) | |
| self.assertEqual(Sequence.generic_validate('ACTGactgee', '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 0) | |
| seq = ' 1 ACTGactgAC aaatttccca ACTGactgaa aaatttccca\n 41 ACTGactgAA aaatttccca ACTGactgtt aaatttccca\n 81 ACTGactgGG aaatttccca ACTGactgcc aaatt' | |
| self.assertEqual(Sequence.generic_validate(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 1) | |
| # not allowed symbol e | |
| seq = ' 1 ACTGactgAC aaatttccca ACTGactgee aaatttccca\n 41 ACTGactgAA aaatttccca ACTGactgtt aaatttccca\n 81 ACTGactgGG aaatttccca ACTGactgcc aaatt' | |
| self.assertEqual(Sequence.generic_validate(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 0) | |
| # not allowed symbol e + len < | |
| seq = ' 1 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 51 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 81 ACTGactgee aaatttccca ACTGactgee aaatt' | |
| self.assertEqual(Sequence.generic_validate(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 0) | |
| # not allowed symbol e + len > | |
| seq = ' 1 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 31 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 81 ACTGactgee aaatttccca ACTGactgee aaatt' | |
| self.assertEqual(Sequence.generic_validate(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 0) | |
| # len > | |
| seq = ' 1 ACTGactgTT aaatttcc ACTGactgAa aaatttccca\n 31 ACTGactgcT aaatttccca ACTGactgCT aaatttccca\n 81 ACTGactgAg aaatttccca ACTGactggg aaatt' | |
| self.assertEqual(Sequence.generic_validate(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 0) | |
| # len < | |
| seq = ' 1 ACTGactgTT aaatttcc ACTGactgAa aaatttccca\n 51 ACTGactgcT aaatttccca ACTGactgCT aaatttccca\n 81 ACTGactgAg aaatttccca ACTGactggg aaatt' | |
| self.assertEqual(Sequence.generic_validate(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 0) | |
| # last len > | |
| seq = ' 1 ACTGactgTT aaatttcc ACTGactgAa aaatttccca\n 51 ACTGactgcT aaatttccca ACTGactgCT aaatttccca\n 81 ACTGactgAg aaatttccca ACTGactggg aaattaaattaaatt' | |
| self.assertEqual(Sequence.generic_validate(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 0) | |
| # last bad symbol | |
| seq = ' 1 ACTGactgTT aaatttcc ACTGactgAa aaatttccca\n 41 ACTGactgcT aaatttccca ACTGactgCT aaatttccca\n 81 ACTGactgAg aaatttccca ACTGactggg aaatte' | |
| self.assertEqual(Sequence.generic_validate(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), 0) | |
| def test_detailed_validate_generic(self): | |
| self.assertEqual(Sequence.detailed_validate_generic('ACTGactg', '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), []) | |
| seq = ' 1 ACTGactgAC aaatttccca ACTGactgaa aaatttccca\n 41 ACTGactgAA aaatttccca ACTGactgtt aaatttccca\n 81 ACTGactgGG aaatttccca ACTGactgcc aaatt' | |
| self.assertEqual(Sequence.detailed_validate_generic(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), []) | |
| seq = ' 1 ACTGactgAC aaatttccca ACTGactgee aaatttccca\n 41 ACTGactgAA aaatttccca ACTGactgtt aaatttccca\n 81 ACTGactgGG aaatttccca ACTGactgcc aaatt' | |
| self.assertEqual(Sequence.detailed_validate_generic(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), ['line 1: block 3 contains illegal chars']) | |
| seq = ' 1 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 51 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 81 ACTGactgee aaatttccca ACTGactgee aaatt' | |
| message = [ | |
| 'line 1: bad line length', | |
| 'line 1: block 1 contains illegal chars', | |
| 'line 1: block 3 contains illegal chars', | |
| 'line 2: bad line length', | |
| 'line 2: block 1 contains illegal chars', | |
| 'line 2: block 3 contains illegal chars', | |
| 'line 3: block 1 contains illegal chars', | |
| 'line 3: block 3 contains illegal chars', | |
| ] | |
| self.assertEqual(Sequence.detailed_validate_generic(seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]'), message) | |
| #def test_translate2protein_in_range_generic(self): | |
| def translate2protein_generic(self): | |
| tdict = { | |
| 'GCA':'A','GCC':'A','GCG':'A','GCT':'A', 'TGC':'C','TGT':'C', 'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E', | |
| 'TTC':'F', 'TTT':'F', 'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', 'CAC':'H', 'CAT':'H', 'ATA':'I', 'ATC':'I', 'ATT':'I', | |
| 'AAA':'K', 'AAG':'K', 'TTA':'L', 'TTG':'L', 'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', 'ATG':'M', 'AAC':'N', 'AAT':'N', | |
| 'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', 'CAA':'Q', 'CAG':'Q', 'AGA':'R', 'AGG':'R', 'CGA':'R', 'CGC':'R', 'CGG':'R', | |
| 'CGT':'R', 'AGC':'S', 'AGT':'S', 'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T', | |
| 'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 'TGG':'W', 'TAC':'Y', 'TAT':'Y', 'TAG': '*', 'TGA':'*', 'TAA':'*' | |
| } | |
| test = 'ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGCTTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGGGATCAGCATTGGCGGAATTACCGACAGTTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGGCCGTTTTTGTTGGATAAAAGACCCACAGGGCGCCATTATTGCGGCCATTAGCTATTTAAAACGTTGATGTAA' | |
| f1 = ('','MESAFNTAGALSWHELTTNNTEEAMRFYAEIFGWHFKTVKMPHGHYHIIENEGISIGGITDSLIPTLPSHWTGYITVNDVDQVAISAKKLGGDILFGPEDIPEVGRFCWIKDPQGAIIAAISYLKR*C','AA') | |
| f2 = ('A','WNRLLILQGR*VGMNSQPIIPKRPCASMLRFLAGTLKPSKCPTVTITLLKTRGSALAELPTV*SPPFPHIGLAILPLTMWIKWLSVLKNSAVTFCLALKTFQRWAVFVG*KTHRAPLLRPLAI*NVDV','A') | |
| f3 = ('AT','GIGF*YCRGVKLA*THNQ*YRRGHALLC*DFWLAL*NRQNAPRSLSHY*KRGDQHWRNYRQFNPHPSLTLDWLYYR*RCGSSGYQC*KTRR*HSVWP*RHSRGGPFLLDKRPTGRHYCGH*LFKTLM*','') | |
| self.assertEqual([f1,f2,f3], Sequence.translate2protein_generic(test, tdict)) | |
| def test_translate2protein(self): | |
| test = 'ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGCTTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGGGATCAGCATTGGCGGAATTACCGACAGTTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGGCCGTTTTTGTTGGATAAAAGACCCACAGGGCGCCATTATTGCGGCCATTAGCTATTTAAAACGTTGATGTAA' | |
| c = Sequence('>name', test) | |
| def test_validate_seq(self): | |
| c = Sequence('>name', 'ACTGactg') | |
| self.assertEqual(c.validate_seq(), 1) | |
| c = Sequence('>name', 'ACTGactgee') | |
| self.assertEqual(c.validate_seq(), 0) | |
| c = Sequence('>name', ' 1 ACTGactgAC aaatttccca ACTGactgaa aaatttccca\n 41 ACTGactgAA aaatttccca ACTGactgtt aaatttccca\n 81 ACTGactgGG aaatttccca ACTGactgcc aaatt') | |
| self.assertEqual(c.validate_seq(), 1) | |
| # not allowed symbol e | |
| c = Sequence('>name', ' 1 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 41 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 81 ACTGactgee aaatttccca ACTGactgee aaatt') | |
| self.assertEqual(c.validate_seq(), 0) | |
| # not allowed symbol e + len < | |
| c = Sequence('>name', ' 1 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 51 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 81 ACTGactgee aaatttccca ACTGactgee aaatt') | |
| self.assertEqual(c.validate_seq(), 0) | |
| # not allowed symbol e + len > | |
| c = Sequence('>name', ' 1 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 31 ACTGactgee aaatttccca ACTGactgee aaatttccca\n 81 ACTGactgee aaatttccca ACTGactgee aaatt') | |
| self.assertEqual(c.validate_seq(), 0) | |
| # len > | |
| c = Sequence('>name', ' 1 ACTGactgTT aaatttcc ACTGactgAa aaatttccca\n 31 ACTGactgcT aaatttccca ACTGactgCT aaatttccca\n 81 ACTGactgAg aaatttccca ACTGactggg aaatt') | |
| self.assertEqual(c.validate_seq(), 0) | |
| # len < | |
| c = Sequence('>name', ' 1 ACTGactgTT aaatttcc ACTGactgAa aaatttccca\n 51 ACTGactgcT aaatttccca ACTGactgCT aaatttccca\n 81 ACTGactgAg aaatttccca ACTGactggg aaatt') | |
| self.assertEqual(c.validate_seq(), 0) | |
| # last len > | |
| c = Sequence('>name', ' 1 ACTGactgTT aaatttcc ACTGactgAa aaatttccca\n 51 ACTGactgcT aaatttccca ACTGactgCT aaatttccca\n 81 ACTGactgAg aaatttccca ACTGactggg aaattaaattaaatt') | |
| self.assertEqual(c.validate_seq(), 0) | |
| # last bad symbol | |
| c = Sequence('>name', ' 1 ACTGactgTT aaatttcc ACTGactgAa aaatttccca\n 41 ACTGactgcT aaatttccca ACTGactgCT aaatttccca\n 81 ACTGactgAg aaatttccca ACTGactggg aaatte') | |
| self.assertEqual(c.validate_seq(), 0) | |
| def test_cmp(self): | |
| c = Sequence('>name', ' 1 ACTG') | |
| o = Sequence('>name2', ' 1 ACTG') | |
| self.assertTrue(c.seq == o.seq) | |
| def test_cut(self): | |
| c = Sequence('>name', ' 1 ACTG') | |
| c.normalize() | |
| cl = [Sequence('>name_frag_1:1', 'A'),Sequence('>name_frag_2:2', 'C'),Sequence('>name_frag_3:3', 'T'),Sequence('>name_frag_4:4', 'G')] | |
| rcl = c.cut(1,1) | |
| self.assertEqual(str(cl[0]), str(rcl[0])) | |
| self.assertEqual(str(cl[1]), str(rcl[1])) | |
| #self.assertEqual(cl[0], rcl[0]) | |
| #self.assertEqual(cl, rcl) | |
| def test_revers(self): | |
| c = Sequence('>name', ' 1 ACTG') | |
| r = Sequence('>rev_name', 'CAGT') | |
| self.assertEqual(str(r), str(c.reverse())) | |
| def test_normalise(self): | |
| c = Sequence('>name', ' 1 ACTG') | |
| self.assertEqual('>name\n 1 ACTG\n', str(c) ) | |
| c.normalize() | |
| self.assertEqual('>name\nACTG\n', str(c) ) | |
| def test_statistics(self): | |
| c = Sequence('>name', ' 1 ACTG') | |
| #r = {'A':1, 'C':1, 'T':1, 'G':1, 'N':0 'L':9} | |
| self.assertEqual({'A':1, 'C':1, 'T':1, 'G':1, 'N':0, 'L':4}, c.statistics()) | |
| c = Sequence('>name', ' 1 ACTG NNNNNNNN') | |
| self.assertEqual({'A':1, 'C':1, 'T':1, 'G':1, 'N':8, 'L':12}, c.statistics()) | |
| c = Sequence('>name', ' 1 ACTG NNNNNNNN\naaanan') | |
| self.assertEqual({'A':5, 'C':1, 'T':1, 'G':1, 'N':10, 'L':18}, c.statistics()) | |
| def test_find_primers(self): | |
| test = 'ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGC' | |
| c = Sequence('>test', test) | |
| self.assertEqual(['GGAATCGGCTTTTAATACTGCAGGGG'],c.find_primers('GGAA', 'GGGG', 'FF')) | |
| self.assertEqual(['AATCGGCT','AATACT','AAGTTGGCATGAACT','AACT','AACGCCCCT'],c.find_primers('AA', 'CT', 'ff')) | |
| def test_find_aprox_motif(self): | |
| test = 'ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGC' | |
| c = Sequence('>test', test) | |
| #print c.find_aprox_motif('TGGAATCGGCT',1) | |
| self.assertEqual(['TGGAATCGGCT'], c.find_aprox_motif('TGGAATCGGCT',1)) | |
| self.assertEqual(['TGGAATCGGCT'], c.find_aprox_motif('TAGAATCGGCT', 1)) | |
| self.assertEqual([], c.find_aprox_motif('TAGAATCGGCT', 0)) | |
| self.assertEqual(['TGGAATCGGCT'], c.find_aprox_motif('TGGAATCGGCT',0)) | |
| def test_find_primers(self): | |
| test = 'ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGCTTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGGGATCAGCATTGGCGGAATTACCGACAGTTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGGCCGTTTTTGTTGGATAAAAGACCCACAGGGCGCCATTATTGCGGCCATTAGCTATTTAAAACGTTGATGTAA' | |
| c = Sequence('>test', test) | |
| t_TTT_GGG_FF = [ | |
| 'TTTTAATACTGCAGGG', | |
| 'TTTAATACTGCAGGG', | |
| 'TTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGG', | |
| 'TTTGGCCCTGAAGACATTCCAGAGGTGGG', | |
| 'TTTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTAAATAGCTAATGGCCGCAATAATGGCGCCCTGTGGG', | |
| 'TTTAAATAGCTAATGGCCGCAATAATGGCGCCCTGTGGG', | |
| 'TTTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTCAATAATGTGATAGTGACCGTGGG', | |
| 'TTTCAATAATGTGATAGTGACCGTGGG' | |
| ] | |
| t_TTT_CCC_FR = [ | |
| 'TTTTAATACTGCAGGG', | |
| 'TTTAATACTGCAGGG', | |
| 'TTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGG', | |
| 'TTTGGCCCTGAAGACATTCCAGAGGTGGG', | |
| 'TTTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTAAATAGCTAATGGCCGCAATAATGGCGCCCTGTGGG', | |
| 'TTTAAATAGCTAATGGCCGCAATAATGGCGCCCTGTGGG', | |
| 'TTTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTCAATAATGTGATAGTGACCGTGGG', | |
| 'TTTCAATAATGTGATAGTGACCGTGGG' | |
| ] | |
| self.assertEqual(t_TTT_GGG_FF, c.find_primers('TTT', 'GGG', 'FF', 0,10000)) | |
| self.assertEqual(t_TTT_CCC_FR, c.find_primers('TTT', 'CCC', 'FR', 0,10000)) | |
| def test_find_aprox_primers(self): | |
| test = 'ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGCTTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGGGATCAGCATTGGCGGAATTACCGACAGTTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGGCCGTTTTTGTTGGATAAAAGACCCACAGGGCGCCATTATTGCGGCCATTAGCTATTTAAAACGTTGATGTAA' | |
| c = Sequence('>test', test) | |
| t_TTT_GGG_FF = [ | |
| 'TTTTAATACTGCAGGG', | |
| 'TTTAATACTGCAGGG', | |
| 'TTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGG', | |
| 'TTTGGCCCTGAAGACATTCCAGAGGTGGG', | |
| 'TTTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTAAATAGCTAATGGCCGCAATAATGGCGCCCTGTGGG', | |
| 'TTTAAATAGCTAATGGCCGCAATAATGGCGCCCTGTGGG', | |
| 'TTTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTCAATAATGTGATAGTGACCGTGGG', | |
| 'TTTCAATAATGTGATAGTGACCGTGGG' | |
| ] | |
| t_TTT_CCC_FR = [ | |
| 'TTTTAATACTGCAGGG', | |
| 'TTTAATACTGCAGGG', | |
| 'TTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGG', | |
| 'TTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGG', | |
| 'TTTGGCCCTGAAGACATTCCAGAGGTGGG', | |
| 'TTTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTAAATAGCTAATGGCCGCAATAATGGCGCCCTGTGGG', | |
| 'TTTAAATAGCTAATGGCCGCAATAATGGCGCCCTGTGGG', | |
| 'TTTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGGG', | |
| 'TTTTCAATAATGTGATAGTGACCGTGGG', | |
| 'TTTCAATAATGTGATAGTGACCGTGGG' | |
| ] | |
| self.assertEqual(t_TTT_GGG_FF, c.find_aprox_primers('TTT', 'GGG', 'FF', 0,0,10000)) | |
| self.assertEqual(t_TTT_CCC_FR, c.find_aprox_primers('TTT', 'CCC', 'FR', 0,0,10000)) | |
| t_TTTT_GGGG_FF = [ | |
| 'CTTTTAATACTGCAGGG', | |
| 'TTTTAATACTGCAGGG', | |
| 'TTTAATACTGCAGGG', | |
| 'TTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'ATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'CTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTATTGAAAACGAGG', | |
| 'TATTGAAAACGAGG', | |
| 'GTTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGG', | |
| 'TTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGG', | |
| 'TATTACCGTTAACGATGTGG', | |
| 'TTCTGTTTGGCCCTGAAGACATTCCAGAGG', | |
| 'TGTTTGGCCCTGAAGACATTCCAGAGG', | |
| 'GTTTGGCCCTGAAGACATTCCAGAGG', | |
| 'TTTGGCCCTGAAGACATTCCAGAGG', | |
| 'GTTTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTTGTTGGATAAAAGACCCACAGGG', | |
| 'TTGTTGGATAAAAGACCCACAGGG', | |
| 'TGTTGGATAAAAGACCCACAGGG', | |
| 'TTATTGCGG', | |
| 'TATTGCGG', | |
| 'GTTTTAAATAGCTAATGGCCGCAATAATGGCG', | |
| 'TTTTAAATAGCTAATGGCCGCAATAATGGCG', | |
| 'TTTAAATAGCTAATGGCCGCAATAATGGCG', | |
| 'TCTTTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'CTTTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TTATCCAACAAAAACGGCCCACCTCTGGAATGTCTTCAGGG', | |
| 'TCTTCAGGG', | |
| 'GTTTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'GTTTTCAATAATGTGATAGTGACCGTGG', | |
| 'TTTTCAATAATGTGATAGTGACCGTGG', | |
| 'TTTCAATAATGTGATAGTGACCGTGG', | |
| ] | |
| self.assertEqual(t_TTTT_GGGG_FF, c.find_aprox_primers('TTTT', 'GGGG', 'FF', 1,0,10000)) | |
| self.assertEqual(t_TTTT_GGGG_FF, c.find_aprox_primers('TTTT', 'CCCC', 'FR', 1,0,10000)) | |
| self.assertEqual(c.find_aprox_primers('TTTT', 'CCCC', 'fr', 1,0,10000), c.find_aprox_primers('TTTT', 'CCCC', 'FR', 1,0,10000)) | |
| self.assertEqual(c.find_aprox_primers('TTTT', 'CCCC', 'Fr', 1,0,10000), c.find_aprox_primers('TTTT', 'CCCC', 'FR', 1,0,10000)) | |
| self.assertEqual(c.find_aprox_primers('TTTT', 'CCCC', 'fR', 1,0,10000), c.find_aprox_primers('TTTT', 'CCCC', 'FR', 1,0,10000)) | |
| t_TTTT_GGGG_FF_60 = [ | |
| 'TTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'ATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'GTTTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| ] | |
| self.assertEqual(t_TTTT_GGGG_FF_60, c.find_aprox_primers('TTTT', 'CCCC', 'FR', 1,60,10000)) | |
| t_TTTT_GGGG_FF_60_65 = [ | |
| 'TTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGG', | |
| 'TTTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| 'TTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG', | |
| ] | |
| #for r in c.find_aprox_primers('TTTT', 'GGGG', 'FF', 1,60,65): | |
| # print r | |
| self.assertEqual(t_TTTT_GGGG_FF_60_65, c.find_aprox_primers('TTTT', 'CCCC', 'FR', 1,60,65)) | |
| def test_leave_name_after_marker(self): | |
| c = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA') | |
| self.assertEqual(1, c.leave_name_after_marker('gene=', 20)) | |
| self.assertEqual('>gene=qwerty_ready', c.name) | |
| #self.assertEqual() | |
| c2 = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA') | |
| self.assertEqual(1, c2.leave_name_after_marker('gene=', 11)) | |
| self.assertEqual('>gene=qwerty', c2.name) | |
| c = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA') | |
| self.assertEqual(1, c.leave_name_after_marker('gene=')) | |
| self.assertEqual('>gene=qwerty_ready', c.name) | |
| c2 = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA') | |
| self.assertEqual(1, c2.leave_name_after_marker('gene=', 6, 0)) | |
| self.assertEqual('>qwerty', c2.name) | |
| def test_cut_name(self): | |
| c = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA') | |
| c.cut_name(5) | |
| self.assertEqual('>test', c.name) | |
| c.cut_name(10) | |
| self.assertEqual('>test', c.name) | |
| if __name__ == "__main__": | |
| unittest.main() |