def test005_findBestCandidateTar2(self):
from dnaSequencing import findBestCandidate
tar2 = 'CATTATTATGAGGTTTCCCTCCCTAAACTT'
can2 = [
'CCACGGGAATCCATAGTCAGAAATAGTATC', 'ACGACCGTTAACCACATTACCCCGTGGTCG',
'ACCCCTAGCCGGCCGATAGAGTGTAAGGAT', 'CGTCGACAGACCACGTTATTTCATTCGGCG',
'CCCTAGCCGGCCGATAGAGTGTAAGGATAG', 'TATGAACTTCGGCGGGTACATATGGACTAT',
'AGTCAGTGTAAGGTTAACTCCGCATTAGAA', 'AGGCTATGCGCAAGAAAAGCCATACTTCTT',
'CTGTCTTCGCCGGGCTCTATTACGGTCGCT', 'AGGGCCTGGAGACAGTCAGTGTAAGGTTAA',
'AACGGAGACGCTTTGCCGTACGACTGACCC', 'CACGGTTATGGCTTCTAGCGGTCTTCACCC',
'AGGCGTCCCTCCTTAGAGGCCAGGTGTCCG', 'GTTTGCGTCTGGAGGATGAAGCACTATACG',
'CTGTGTATGAACTTCGGCGGGTACATATGG', 'CGGTCTTCACCCCCCCAGGCAAGTAGCTTC',
'TAATGTCCATGGTGATACCCCTAGCCGGCC', 'CACCCCCCCAGGCAAGTAGCTTCACGCTGA',
'GCGTTTCAGAGCATTAATCGGGGGCCGTGT', 'CCCGACACCGGCCTTGCAGGCTATGCGCAA',
'GACCCCAAGGGGCGATATTGCACGACCGTT', 'TCGAGCGATAATTGGTGTTCGTTACAGCGT',
'GGATAGCAGACCCCCACCTTCGTAAAACAA', 'CCCTCCTTAGAGGCCAGGTGTCCGAACTTC',
'TCAGAAATAGTATCACTCCTTATTCCGACT', 'CCCGTGTTAGGCGTCCCTCCTTAGAGGCCA',
'GTCTCTTGCGCTTAAATAATCCAGCATCGC', 'CTCCCGTCGACAGACCACGTTATTTCATTC',
'CAGACCACGTTATTTCATTCGGCGTTTCTC', 'TAGTATCACTCCTTATTCCGACTCAGAAAG',
'CGGACGACCTCTAGGATGTACTACCCTACT', 'ACCGAGAACCGCGGTTATAATTTCACATTA',
'CAGTGTAAGGTTAACTCCGCATTAGAAGCC', 'ATGGCTTCTAGCGGTCTTCACCCCCCCAGG',
'CGAGAACCGCGGTTATAATTTCACATTATT', 'GCATCGCCTAGCAAAGCAGCTTACGTTCAG',
'CAAATCTCACTAATGTCCATGGTGATACCC', 'GGGAATCCATAGTCAGAAATAGTATCACTC',
'GTTTGCGTCTGGAGGATGAAGCACTATACG'
]
self.assertTupleEqual(findBestCandidate(tar2, can2),
('TATGAACTTCGGCGGGTACATATGGACTAT', 1))
def test003_findBestCandidateTar0(self):
from dnaSequencing import findBestCandidate
tar0 = 'TTATAGTGATATACGTGCTTAGGTAGTGCAGAGACACAACTTATAGAGTGAGGCCAGCTCACGAGCTCTAGAAGCCCAAA'
can0 = [
'TATTGTGCTCTATAGCTCCAGGCACATCCCTTGACGGATTGGGGACTGTCTTGACGAAAGTTCGGAGGTAGAAAAGTCCA',
'GACGACACCCTGGCAAAGGTCACGTCATGGGTGGAGTACTTATACCGGCAGCAGAGCGATCTGCTACCTATCTTCATGAT',
'CACGAGCTCTAGAAGCCCAAACTGTGACGCAATTGCCGGGCTAAAACTATGCTAAGAAATCCCCATTACCAGAGTCTTAG',
'TGAGCCGTTGGGCAGTTAACGGATTTTACTCGTCGCTGCCTGAAGTGCCAAATTTACCAAAAACCGGATAACTTCATGCA',
'CTTATAGAGTGAGGCCAGCTCACGAGCTCTAGAAGCCCAAATTGCTACTGTGCCGCTGCGCACCGCATGATCGCAGTCAG',
'TTAGAGGAATTGGACGGCACTCGGACACAAGCTCACGCCCCATACTTTAGCACCGAATATCGACTAAGCATAGTTGATCT',
'AGCAAGAGTTGGTATCTCTAGGGGCTTCTCCGGACGCAACGACGCGTCTGACAGTTCAGGTTGTTATGACCCGGGTGTGA',
'CTATGGTTAGGCAACTTCCACGCTATCCCTCGACCACGGCTCGTGGAGCCGTACCGGTGTATTTTGTTGCTGCTAATATT',
'GTAGCACGCAGTTCGAGTCACCCGGAAGCAGCGAAACGTTCGGCAACTACAAACTCCAATCTTGTATTCGGGTGCCTTTT',
'CGATTGTCTGTGTTCTGCATGAGCACAATAAGTACAAGTCGAACTGGTATTTACTAAAGTCCGCATATTGTACGGTACGT'
]
self.assertTupleEqual(findBestCandidate(tar0, can0), (
'CTTATAGAGTGAGGCCAGCTCACGAGCTCTAGAAGCCCAAATTGCTACTGTGCCGCTGCGCACCGCATGATCGCAGTCAG',
41))
def test004_findBestCandidateTar1(self):
from dnaSequencing import findBestCandidate
tar1 = 'GTCGCGTTCAGGCGCATTAAGTTAGTCGGA'
can1 = [
'TCAGGCGCATTAAGTTAGTCGGAGCACACG', 'TGCTCTGGTCGCGTTCAGGCGCATTAAGTT',
'GCGCATTAAGTTAGTCGGAGCACACGATAG', 'GATGGGATTCCACTGCTCTGGTCGCGTTCA',
'AGATGGGATTCCACTGCTCTGGTCGCGTTC', 'CGTTCAGGCGCATTAAGTTAGTCGGAGCAC',
'CTAAGATGGGATTCCACTGCTCTGGTCGCG', 'TACATGAAGCGCTACGTCTTATTGCGCTGG',
'TCGGAGCACACGATAGTGTACATGAAGCGC', 'TCGCGTTCAGGCGCATTAAGTTAGTCGGAG',
'ACGATAGTGTACATGAAGCGCTACGTCTTA', 'GATGGGATTCCACTGCTCTGGTCGCGTTCA',
'TTCAGGCGCATTAAGTTAGTCGGAGCACAC', 'AGTTAGTCGGAGCACACGATAGTGTACATG',
'TCGGAGCACACGATAGTGTACATGAAGCGC', 'TAGTGTACATGAAGCGCTACGTCTTATTGC',
'GATTCCACTGCTCTGGTCGCGTTCAGGCGC', 'TGTACATGAAGCGCTACGTCTTATTGCGCT',
'TGCTCTGGTCGCGTTCAGGCGCATTAAGTT', 'TTAGTCGGAGCACACGATAGTGTACATGAA',
'TACATGAAGCGCTACGTCTTATTGCGCTGG', 'GATTCCACTGCTCTGGTCGCGTTCAGGCGC',
'AGTCGGAGCACACGATAGTGTACATGAAGC', 'TAGTGTACATGAAGCGCTACGTCTTATTGC',
'CACTAAGATGGGATTCCACTGCTCTGGTCG', 'GATAGTGTACATGAAGCGCTACGTCTTATT',
'TGGTCGCGTTCAGGCGCATTAAGTTAGTCG', 'AAGTTAGTCGGAGCACACGATAGTGTACAT',
'AGTGTACATGAAGCGCTACGTCTTATTGCG', 'AAGATGGGATTCCACTGCTCTGGTCGCGTT',
'GGCGCATTAAGTTAGTCGGAGCACACGATA', 'AAGATGGGATTCCACTGCTCTGGTCGCGTT',
'ACACGATAGTGTACATGAAGCGCTACGTCT', 'CACTAAGATGGGATTCCACTGCTCTGGTCG',
'AAGTTAGTCGGAGCACACGATAGTGTACAT', 'GTTCAGGCGCATTAAGTTAGTCGGAGCACA',
'CTGCTCTGGTCGCGTTCAGGCGCATTAAGT', 'GGGATTCCACTGCTCTGGTCGCGTTCAGGC',
'GTCGGAGCACACGATAGTGTACATGAAGCG', 'GGAGCACACGATAGTGTACATGAAGCGCTA',
'ACTAAGATGGGATTCCACTGCTCTGGTCGC', 'GATAGTGTACATGAAGCGCTACGTCTTATT',
'CATTAAGTTAGTCGGAGCACACGATAGTGT', 'GATGGGATTCCACTGCTCTGGTCGCGTTCA',
'AGTGTACATGAAGCGCTACGTCTTATTGCG', 'TCGGAGCACACGATAGTGTACATGAAGCGC',
'ACACGATAGTGTACATGAAGCGCTACGTCT', 'ACTGCTCTGGTCGCGTTCAGGCGCATTAAG',
'ACGATAGTGTACATGAAGCGCTACGTCTTA', 'GCACACGATAGTGTACATGAAGCGCTACGT',
'GATAGTGTACATGAAGCGCTACGTCTTATT', 'TCGCGTTCAGGCGCATTAAGTTAGTCGGAG',
'CTGCTCTGGTCGCGTTCAGGCGCATTAAGT', 'GTACATGAAGCGCTACGTCTTATTGCGCTG',
'ATTAAGTTAGTCGGAGCACACGATAGTGTA', 'CACACGATAGTGTACATGAAGCGCTACGTC',
'GGGATTCCACTGCTCTGGTCGCGTTCAGGC', 'TGCTCTGGTCGCGTTCAGGCGCATTAAGTT',
'TCTGGTCGCGTTCAGGCGCATTAAGTTAGT', 'AGATGGGATTCCACTGCTCTGGTCGCGTTC',
'ATAGTGTACATGAAGCGCTACGTCTTATTG', 'AGGCGCATTAAGTTAGTCGGAGCACACGAT',
'ACGATAGTGTACATGAAGCGCTACGTCTTA', 'AGGCGCATTAAGTTAGTCGGAGCACACGAT',
'TCAGGCGCATTAAGTTAGTCGGAGCACACG', 'CGCGTTCAGGCGCATTAAGTTAGTCGGAGC',
'GGATTCCACTGCTCTGGTCGCGTTCAGGCG', 'TGGGATTCCACTGCTCTGGTCGCGTTCAGG',
'TAAGATGGGATTCCACTGCTCTGGTCGCGT', 'ACGATAGTGTACATGAAGCGCTACGTCTTA',
'GAGCACACGATAGTGTACATGAAGCGCTAC', 'ATTCCACTGCTCTGGTCGCGTTCAGGCGCA',
'GCTCTGGTCGCGTTCAGGCGCATTAAGTTA', 'AGCACACGATAGTGTACATGAAGCGCTACG',
'GCGTTCAGGCGCATTAAGTTAGTCGGAGCA', 'CGCGTTCAGGCGCATTAAGTTAGTCGGAGC',
'GTCGGAGCACACGATAGTGTACATGAAGCG', 'GATTCCACTGCTCTGGTCGCGTTCAGGCGC',
'TAAGATGGGATTCCACTGCTCTGGTCGCGT', 'GATTCCACTGCTCTGGTCGCGTTCAGGCGC',
'TAGTCGGAGCACACGATAGTGTACATGAAG', 'AAGTTAGTCGGAGCACACGATAGTGTACAT',
'TCGGAGCACACGATAGTGTACATGAAGCGC', 'ACGATAGTGTACATGAAGCGCTACGTCTTA',
'TAGTCGGAGCACACGATAGTGTACATGAAG', 'TTAGTCGGAGCACACGATAGTGTACATGAA',
'CACACGATAGTGTACATGAAGCGCTACGTC', 'GCACACGATAGTGTACATGAAGCGCTACGT',
'TCGGAGCACACGATAGTGTACATGAAGCGC', 'AGCACACGATAGTGTACATGAAGCGCTACG',
'ACACGATAGTGTACATGAAGCGCTACGTCT', 'CACACGATAGTGTACATGAAGCGCTACGTC',
'AGATGGGATTCCACTGCTCTGGTCGCGTTC', 'CGTTCAGGCGCATTAAGTTAGTCGGAGCAC',
'TAGTGTACATGAAGCGCTACGTCTTATTGC', 'GATGGGATTCCACTGCTCTGGTCGCGTTCA',
'TAGTCGGAGCACACGATAGTGTACATGAAG', 'TGGTCGCGTTCAGGCGCATTAAGTTAGTCG',
'AGTCGGAGCACACGATAGTGTACATGAAGC', 'CCACTGCTCTGGTCGCGTTCAGGCGCATTA',
'CTCTGGTCGCGTTCAGGCGCATTAAGTTAG', 'TGCTCTGGTCGCGTTCAGGCGCATTAAGTT',
'TGCTCTGGTCGCGTTCAGGCGCATTAAGTT', 'TAAGATGGGATTCCACTGCTCTGGTCGCGT',
'TGCTCTGGTCGCGTTCAGGCGCATTAAGTT', 'GCATTAAGTTAGTCGGAGCACACGATAGTG',
'GCGTTCAGGCGCATTAAGTTAGTCGGAGCA', 'ATTCCACTGCTCTGGTCGCGTTCAGGCGCA',
'GTGTACATGAAGCGCTACGTCTTATTGCGC', 'ATAGTGTACATGAAGCGCTACGTCTTATTG',
'TAAGATGGGATTCCACTGCTCTGGTCGCGT', 'GTTCAGGCGCATTAAGTTAGTCGGAGCACA',
'GATTCCACTGCTCTGGTCGCGTTCAGGCGC', 'TAGTGTACATGAAGCGCTACGTCTTATTGC',
'AGCACACGATAGTGTACATGAAGCGCTACG', 'ATGGGATTCCACTGCTCTGGTCGCGTTCAG',
'GTTAGTCGGAGCACACGATAGTGTACATGA', 'TAAGTTAGTCGGAGCACACGATAGTGTACA',
'TGTACATGAAGCGCTACGTCTTATTGCGCT', 'TTAGTCGGAGCACACGATAGTGTACATGAA',
'GGTCGCGTTCAGGCGCATTAAGTTAGTCGG', 'AGTCGGAGCACACGATAGTGTACATGAAGC',
'GGTCGCGTTCAGGCGCATTAAGTTAGTCGG', 'GAGCACACGATAGTGTACATGAAGCGCTAC',
'AGTTAGTCGGAGCACACGATAGTGTACATG', 'ACACGATAGTGTACATGAAGCGCTACGTCT',
'GCACACGATAGTGTACATGAAGCGCTACGT', 'CTCTGGTCGCGTTCAGGCGCATTAAGTTAG',
'GCTCTGGTCGCGTTCAGGCGCATTAAGTTA', 'AGTGTACATGAAGCGCTACGTCTTATTGCG',
'GTTCAGGCGCATTAAGTTAGTCGGAGCACA', 'TCAGGCGCATTAAGTTAGTCGGAGCACACG',
'GCACTAAGATGGGATTCCACTGCTCTGGTC'
]
self.assertTupleEqual(findBestCandidate(tar1, can1),
('TCGCGTTCAGGCGCATTAAGTTAGTCGGAG', 29))
def test007_noMatches(self):
from dnaSequencing import findBestCandidate
self.assertTupleEqual(findBestCandidate('aaa', ['bbb', 'ccc']),
('', 0))
def test002_findBestCandidateTarEasy(self):
from dnaSequencing import findBestCandidate
tar_easy = 'ABCDEFG'
can_easy = ['GHHHHHH', 'FGHHHHH', 'EFGHHHH', 'CDEFGHH', 'DEFGHHH']
self.assertTupleEqual(findBestCandidate(tar_easy, can_easy),
('CDEFGHH', 5))
def test006_findBestCandidateWithEmptyLines(self):
from dnaSequencing import findBestCandidate
tar = 'ABCDEFG'
can = ['', '', 'EFGHHHH', 'CDEFGHH', 'DEFGHHH']
self.assertTupleEqual(findBestCandidate(tar, can), ('CDEFGHH', 5))