def rosalind_RNA():
s = 'AGCAGTGCGGTCTCGGGCCGGCTTGGCTGTCTCGACCGATGTGCGCTCATGCGCGTCGAATGATGATGATACACGTGTTTGACAATTTGTATTCATTAGTTCTGAGC' \
'GAACATTCGTGACGGCGCGGAGTAGCCGGATTAATACTACGTAGTCCCAGTGGTTCGTCGCGGGAGTCCATCAGCGGCAGATACCCGTAGGAAAGCGCTCGTTACGG' \
'TTTGGGCATCCCCCAGACATCTCCGCACCCTGGCCAAGTGGGAACGCCCGTGACTCGCCTTCGCTCGTGGAAGAGCGATAGTTTTTGGTTACAGGTTATTGATTCCG' \
'CATGCACCACGTCCGCTCCACAGAAAGCTTCTACTGCTCGTGCGTTAGACTGCCTCTGGGATGTGACAGATTCGACGGTGACGTAAATGGGACCGCTATAACAAATA' \
'AGGATTAGATGAGATCCGATCTCGTGCGGACTGATCCGACCTCGCCATCACGGCAAGGAGCTAGCCGTGGTCTCTAGTCCTCCACGATCAGTGTTCAATGTGTTGCG' \
'GAACGTACTGCGGCCCAAGTCGGTGCGCTTATCGGATTATCGCGCTACCCAAGCTGGTAGTTAGGACCAGGATGGTCATATTCGGTCATACAAGATGATGATACCGC' \
'AGGCCCAAACCATTCCGATAGAAGCGTAGTCGCGGTGGAGTGCCGTGTACATTCAAGGATCACACGCTGCACATTATATCGCTGAAGCCCACGAAAAAAAATAGCGC' \
'CCCGGACGTAGCGAGCCGTATGCCATTCCTTTCCGTGTGCTAGCCCCCATGAGTTTAGGTCACTGCCCCCAATCGCGCTTTCAGGCTAGTATCAGTTAAGCCACTAA' \
'ACGTGGACACCTACTCTGTCACCATCATTGCTTGGAGAGTTAGATGGGGCCAGGAGCAATTAAATATTGCCGCTAGCCACCATTAACACGAGCCTTACTATTTACT'
print(seq_to_str(transcribe_to_rna(str_to_dna(s))))
def rosalind_REVC():
s = 'GCACGCGTCGACGTGATGCGTTTCTGCACCTAAATAACCTCTTCTGAACCATTTGGGTCATGGGGCGTACACCTGTGGCCTAGATAGCATAAGAAGCATCCGGCAAA' \
'ACAAAATAACCCTTCTTCTGAGGATACCGGAAAAGCAGCCAACAGTTTATGAAGGTAGCCCGATTCTAGAATTGAATCCTCTCTTGACATGAAATAGAGCCGTGTGC' \
'GCGGCTCAAAACCCACTTGGAGACAGAGGCGCGACTTGTAGTTTTATGTCAAATCTGACTGTATCAAGGTCGTCTTGACCGTAGGTATAGAAAGCGAGAAGGTAATT' \
'CCGCGGATGCGCTTTGGTGTACCGTAAATTCACCCCCTTGCAATGAACACAGATATTTGCATAGTGCAACCTCGTTGTCCGAGTCGTAAGCCATTGACTAGCTTCAC' \
'TTGAAACGGGCCCCCCTGCACTTCCCATATGAACAATCTGGTCATGTTTTTCCACCGTTTGGGATTCCTGATATTATACGCGAATCCGCTCGGTGTGGCTGATGCGA' \
'ACGTAGTAGAAACACATGGCACGCTTGAAACAGCCCATATTGGTTCGTGGCATTCATGTTCGCCTAGATATCACTATTTGGAACAATCACCCGCTTCTCTTCGGCAG' \
'GACTACTTAATGTAAAAAGCGGTCGAAATGCGCCTCACATGACTGCAGCACGGGCAGCTCGCCTGGACCGGCGGGGCTAACGTTGTGCGTGTTACATCAACAACAGC' \
'TGCAGAGAAAACAGACCATGATTAAGCCGGCCCCGGGCTTATATGTGATGTGTGCGATCGTTTAGCACCTGAGTCTAAATTTTACATCCTAAACATTAGCTCAGCGC' \
'ATTTGGCCAATCTGTAGATGGGTTACACTTGTTCCGCCAGACCGGCGCATCCAGGGTTACTACGCCTCTC'
dna_forward = str_to_dna(s)
dna_reverse = reverse_complement_dna(dna_forward)
print(seq_to_str(dna_reverse))
def rosalind_DNA():
def rosalind_count_dna(histogram):
return ' '.join(str(histogram[n]) for n in NUCLEOTIDES_DNA)
s = 'GGCAGGAACCCTGTCGGCTTCTCCCCCCTATACGGAAAAAAGTGTGGCAGTGGAAGAAAGACCCACTGCGTTCGGAAAAACTAGCGCTCGAACGCTCGGCAGGGTAA' \
'CGCCTCGGACTGACAGTCTCTAGTATGTCATCCCACAAACCTGACAACGACCCTCCGGGAGAGTCCGAGTCATGAAGGGCGGGCGGCTTTAACAACATCCACTTGCA' \
'CTGAACGCTTTAGACATGGCTTGATGCGCCAGGCCATTGCAATCTTTCTTTGCACACACATTCAGGTGGTTCTCAGTAACTGTAAACGATGAACGAGGCACGCGGTT' \
'CATGATGGTTGCGTGGCAGTATAAAAAACTTAAACGTTCGAAAGGGAGATTTGGTTCGCGTCGCCACGTGCGCGGTATGCGGCTAAACGGCAGACGAACATACTCTT' \
'AGATGCTTTTAGAATCCGGACTAGTATTGCCTGGTATACTGGTGATAGGAGCAGTGCAGTTAGTGTTACCAAAATCACTCACTTCTAAGCCGAGTGTCGGTAAACAG' \
'CACACATGATATCCATGGGCATATTAGCAAGGTCGGACGGGTACCAAGAAAAGTAAGGTGCGTGCCATCAAATTACTGTTTATCGGGTCAGAGATTCTAATGCATGT' \
'TGCGAGGCATGTACTCAACTGTCTTGAGTGGCCAGGATTTGAGGTTGACGAGGGCCTGAAAAATTGTGAGCTTGGTGGGAAGAGAGAGAAGGAGGAGTTCTATTCTG' \
'CATCATGCGGCATCCTCCAGGAGTTCCCGCAATATTTAGTAGGGCGGTCCGGTAGCCCGCTAAGAGACGCCTGAGTGACAGAAATCATGGACGCCCGGCGCGTCACT' \
'ATTAACTAATTAGCTGCATAAGATCGAGCGGACCGTGACGATAAGATCGAAGATGTGAGCTTTCTAAAACAGTGGGGCGGACTTCACGTTTCGAGCGCTGGGCCA'
print(rosalind_count_dna(count_nucleotides(str_to_dna(s))))
def test_count_nucleotides():
dna = str_to_dna('ACCCAACT')
dna_histogram = count_nucleotides(dna)
assert dna_histogram == {
'A': 3,
'C': 4,
'G': 0,
'T': 1,
'U': 0,
}
rna = str_to_rna('ACCCAACU')
rna_histogram = count_nucleotides(rna)
assert rna_histogram == {
'A': 3,
'C': 4,
'G': 0,
'T': 0,
'U': 1,
}
def test_rosalind_03():
s = 'AAAACCCGGT'
dna_forward = str_to_dna(s)
dna_reverse = reverse_complement_dna(dna_forward)
assert seq_to_str(dna_reverse) == 'ACCGGGTTTT'
def test_rosalind_02():
s = 'GATGGAACTTGACTACGTAAATT'
dna = str_to_dna(s)
rna = transcribe_to_rna(dna)
assert seq_to_str(rna) == 'GAUGGAACUUGACUACGUAAAUU'
def test_rosalind_01():
dna = str_to_dna('AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC')
histogram = count_nucleotides(dna)
formated = ' '.join(str(histogram[n]) for n in NUCLEOTIDES_DNA)
assert formated == '20 12 17 21'
def test_transcribe_to_rna():
dna = str_to_dna('GATGGAACTTGACTACGTAAATT')
rna = str_to_rna('GAUGGAACUUGACUACGUAAAUU')
assert transcribe_to_rna(dna) == rna
def test_reverse_complement_dna():
dna_0 = str_to_dna('gattaca')
dna_1 = str_to_dna('tgtaatc')
assert reverse_complement_dna(dna_0) == dna_1
def test_str_to_dna():
s = 'gaTtACa'
assert str_to_dna(s) == [G, A, T, T, A, C, A]
def test_complement_dna():
dna_0 = str_to_dna('gattaca')
dna_1 = str_to_dna('ctaatgt')
assert complement_dna(dna_0) == dna_1