52 lines
1.7 KiB
Text
52 lines
1.7 KiB
Text
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UInt32 seed = 0
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F nonrandom(n)
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:seed = 1664525 * :seed + 1013904223
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R Int(:seed >> 16) % n
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F nonrandom_choice(lst)
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R lst[nonrandom(lst.len)]
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F basecount(dna)
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DefaultDict[Char, Int] d
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L(c) dna
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d[c]++
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R sorted(d.items())
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F seq_split(dna, n = 50)
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R (0 .< dna.len).step(n).map(i -> @dna[i .< i + @n])
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F seq_pp(dna, n = 50)
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L(part) seq_split(dna, n)
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print(‘#5: #.’.format(L.index * n, part))
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print("\n BASECOUNT:")
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V tot = 0
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L(base, count) basecount(dna)
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print(‘ #3: #.’.format(base, count))
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tot += count
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V (base, count) = (‘TOT’, tot)
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print(‘ #3= #.’.format(base, count))
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F seq_mutate(String =dna; count = 1, kinds = ‘IDSSSS’, choice = ‘ATCG’)
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[(String, Int)] mutation
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V k2txt = [‘I’ = ‘Insert’, ‘D’ = ‘Delete’, ‘S’ = ‘Substitute’]
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L 0 .< count
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V kind = nonrandom_choice(kinds)
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V index = nonrandom(dna.len + 1)
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I kind == ‘I’
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dna = dna[0 .< index]‘’nonrandom_choice(choice)‘’dna[index..]
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E I kind == ‘D’ & !dna.empty
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dna = dna[0 .< index]‘’dna[index+1..]
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E I kind == ‘S’ & !dna.empty
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dna = dna[0 .< index]‘’nonrandom_choice(choice)‘’dna[index+1..]
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mutation.append((k2txt[kind], index))
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R (dna, mutation)
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print(‘SEQUENCE:’)
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V sequence = ‘TCAATCATTAATCGATTAATACATTCAATTTGAACATCTCCAGGAGAAGGCAGGGTAATCTCGTGTAGCCGTGCTTGGGGCCTCCGATATGGCCGGGGAATTTCAAAGTATAGTGTGCATCCCCTCATAATACATAGATCTATAGGTAAGTATATGGGTTGACGTTGTTAGATGCGATACACGTGCACACTTTATGAATTTTACGTTCCTCTGCCTAGAGTGCCAAGTTTCAATTTGCTACGGTTCCTCA’
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seq_pp(sequence)
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print("\n\nMUTATIONS:")
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V (mseq, m) = seq_mutate(sequence, 10)
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L(kind, index) m
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print(‘ #10 @#.’.format(kind, index))
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print()
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seq_pp(mseq)
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