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_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_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_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]))
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_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_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 = '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_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 convert_to_fq(self, quality):
nlist = []
i = 1
for r in self.contigs:
q = chr(33+quality)*len(r)
#n = self.name.replace('>', '@')
#n = n.replace(' ','_')
n = '@EAS123:100:FC123VJ:2:'+str(i)+':'+str(i*7)+':'+str(i*8)+' 1:N:18:1'
i += 1
nlist.append(Sequence(n, r.seq, q))
return Fa(nlist, self.name+'_fq')
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 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_cmp(self):
c = Sequence('>name', ' 1 ACTG')
o = Sequence('>name2', ' 1 ACTG')
self.assertTrue(c.seq == o.seq)
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)
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_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 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_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_revers(self):
c = Sequence('>name', ' 1 ACTG')
r = Sequence('>rev_name', 'CAGT')
self.assertEqual(str(r), str(c.reverse()))
def test_translate2protein(self):
test = 'ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGCTTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGGGATCAGCATTGGCGGAATTACCGACAGTTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGGCCGTTTTTGTTGGATAAAAGACCCACAGGGCGCCATTATTGCGGCCATTAGCTATTTAAAACGTTGATGTAA'
c = Sequence('>name', test)
def load_content(content):
ncs = re.findall(re.compile('(?=(^>[\S\s]+?)(^>|\Z))',re.M), content)
contigs_list = []
for r in ncs:
contigs_list.append(Sequence(r[0].split('\n', 1)[0].rstrip(), re.sub('^>.*\n', '', r[0].rstrip())))
return contigs_list
def test_validate_name_string(self):
c = Sequence('>name', 'ACTGactg')
self.assertEqual(c.validate_name_string('>name'), 1)