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Bioinformatics/Sequence mutation: Difference between revisions
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</pre>
=={{header|J}}==
<lang J>ACGT=: 'ACGT'
MUTS=: ;: 'del ins mut'
NB. generate sequence of size y of uniformly selected nucleotides.
NB. represent sequences as ints in range i.4 pretty printed. nuc
NB. defined separately to avoid fixing value inside mutation
NB. functions.
nuc=: monad : '?4'
dna=: nuc"0 @ i.
NB. randomly mutate nucleotide at a random index by deletion insertion
NB. or mutation of a nucleotide.
del=: {.,[:}.}.
ins=: {.,nuc@],}.
mut=: {.,nuc@],[:}.}.
NB. pretty print nucleotides in rows of 50 with numbering
seq=: [: (;~ [: (4&":"0) 50*i.@#) _50]\{&ACGT
sim=: monad define
'n k ws'=. y NB. initial size, mutations, and weights for mutations
ws=. (% +/) ws NB. normalize weights
A=.0$]D0=.D=. dna n NB. initial dna and history of actions
NB. k times do a random action according to weights and record it
for. i.k do.
D=.". action=. (":?#D),' ',(":MUTS{::~(+/\ws)I.?0),' D'
A=. action ; A
end.
echo 'actions';,. A-.a:
echo ('mutation';'probability') , MUTS ,. <"0 ws
('start';'end'),.(seq D0) ,: seq D
)
simulate=: (sim@(1 1 1&; &. |. ))`sim@.(3=#)</lang>
{{out}}
<pre> simulate 200 ; 10
┌─────────┐
│actions │
├─────────┤
│60 mut D │
├─────────┤
│156 del D│
├─────────┤
│44 mut D │
├─────────┤
│64 mut D │
├─────────┤
│167 mut D│
├─────────┤
│40 ins D │
├─────────┤
│39 mut D │
├─────────┤
│187 del D│
├─────────┤
│186 del D│
├─────────┤
│150 del D│
└─────────┘
┌────────┬───────────┐
│mutation│probability│
├────────┼───────────┤
│del │0.333333 │
├────────┼───────────┤
│ins │0.333333 │
├────────┼───────────┤
│mut │0.333333 │
└────────┴───────────┘
┌─────┬────┬──────────────────────────────────────────────────┐
│start│ 0│GGCTGTTGGCCGCCAATCTACAATGATAGCGCGTGAGGAGGGCTAATGTA│
│ │ 50│GAGCCAATAATGGATGCTCGCGCTTCTGCTTATGCTGGTTACTGCTGCCC│
│ │ 100│AAAAACGGGGTACATTGAGCGATAAGCCCGCAAGGTTACTGCTCGTGACA│
│ │ 150│GTCCGAACACCACATTCGTGGTTACTCGACTCTGCCACCTCTTAGCGGAT│
├─────┼────┼──────────────────────────────────────────────────┤
│end │ 0│GGCTGTTGGCCGCCAATCTACAATGATAGCGCGTGAGGACCGGCAAATGT│
│ │ 50│AGAGCCAATACTGGATGCTCGCGCTTCTGCTTATGCTGGTTACTGCTGCC│
│ │ 100│CAAAAACGGGGTACATTGAGCGATAAGCCCGCAAGGTTACTGCTCGTGAC│
│ │ 150│ATCCGACACCACATTCCTGGTTACTCGACTCTGCCACCTTAGCGGAT │
└─────┴────┴──────────────────────────────────────────────────┘
simulate 200 ; 10 ; 1 3 1
┌─────────┐
│actions │
├─────────┤
│120 ins D│
├─────────┤
│199 ins D│
├─────────┤
│138 mut D│
├─────────┤
│15 ins D │
├─────────┤
│8 del D │
├─────────┤
│135 ins D│
├─────────┤
│29 ins D │
├─────────┤
│118 del D│
├─────────┤
│111 ins D│
├─────────┤
│10 del D │
└─────────┘
┌────────┬───────────┐
│mutation│probability│
├────────┼───────────┤
│del │0.2 │
├────────┼───────────┤
│ins │0.6 │
├────────┼───────────┤
│mut │0.2 │
└────────┴───────────┘
┌─────┬────┬──────────────────────────────────────────────────┐
│start│ 0│GAACATACAATATCGTGTGGGTGGTAAGGTGCGCCGATTTGGCAGTGTAG│
│ │ 50│AGCGGCCTCTGGCCGGGCCCATACTGACATATCTTTTATCTCCGTGCTAG│
│ │ 100│CAGAAGAATCAAACGCGTCAAGATGCTGGCGCGGGCTGATATGCGCCCGG│
│ │ 150│CAGTGGAGAACTGCGTTGATACACCTCAAAGATAAGCGGACGATATTAGC│
├─────┼────┼──────────────────────────────────────────────────┤
│end │ 0│GAACATACAATCGTGCTGGGTGGTAAGGTTGCGCCGATTTGGCAGTGTAG│
│ │ 50│AGCGGCCTCTGGCCGGGCCCATACTGACATATCTTTTATCTCCGTGCTAG│
│ │ 100│CAGAAGAATCAACACGCGTAGAGATGCTGGCGCGGGACTGATATGCGCCC│
│ │ 150│GGCAGTGGAGAACTGCGTTGATACACCTCAAAGATAAGCGGACGATATTA│
│ │ 200│GGC │
└─────┴────┴──────────────────────────────────────────────────┘</pre>
=={{header|Julia}}==
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