Bioinformatics/Sequence mutation: Difference between revisions
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T 53</pre>
=={{header|Phix}}==
<lang Phix>string dna = repeat(' ',200+rand(300))
for i=1 to length(dna) do dna[i] = "ACGT"[rand(4)] end for
procedure show()
sequence acgt = repeat(0,5)
for i=1 to length(dna) do
acgt[find(dna[i],"ACGT")] += 1
end for
acgt[$] = sum(acgt)
sequence s = split(trim(join_by(split(join_by(dna,1,10,""),"\n"),1,5," ")),"\n\n")
for i=1 to length(s) do
printf(1,"%3d: %s\n",{(i-1)*50+1,s[i]})
end for
printf(1,"\nBase counts: A:%d, C:%d, G:%d, T:%d, total:%d\n",acgt)
end procedure
procedure mutate()
printf(1,"\n")
for i=1 to 10 do
integer p = rand(length(dna)),
sdi = "SDI"[rand(3)],
rep = "ACGT"[rand(4)],
was = dna[p]
switch sdi do
case 'S':dna[p] = rep printf(1,"swapped %c at %d for %c\n",{was,p,rep})
case 'D':dna[p..p] = "" printf(1,"deleted %c at %d\n",{was,p})
case 'I':dna[p..p-1] = ""&rep printf(1,"inserted %c at %d, before %c\n",{rep,p,was})
end switch
end for
printf(1,"\n")
end procedure
show()
mutate()
show()</lang>
{{out}}
<pre>
1: ATAGACCGAT GTGTAGGTCT CGAACATCCC TGGGGTAGCT CAGCTTGGGG
51: GTTGACCTGT CTTGCTCCCA TGAACTGAGG GATTTGGAAA TAACGCTTAT
101: AACTGCGGGG GATTGATATG GGACATTGTT GCTGTAGGGC TTCGGCGTGC
151: TTAGAAACAA GAGAACACCA ATTTCGATAG ACCAGGTTTC GTCCCGCTAC
201: GAGTGATAGT AGCGCGTTAG GATTAATAAT CAGGGAGAGC ATTAAACATT
251: CTAAAAACTG ACATTCCCGA GGTGGAACCC GAGTTGATAA CGAGTATGCT
301: CTGAAAAATT AATTGATTGA TCCGCGACAC TATCACACCG TCTTCGCCGT
351: TGTAATGCAT GCTGGCTTAG CATCCGGATG CTCTTCTACC GATCTTAAGG
401: CGCGCACTCC CCAAGGAGCA TAGAAGCATC CCCGGCCCTC GACAGAGTCT
451: CCCAGTGTAA GTGTCTTTAT CCAAAATC
Base counts: A:125, C:111, G:120, T:122, total:478
inserted C at 58, before T
deleted T at 2
deleted C at 169
deleted G at 80
inserted A at 331, before T
swapped C at 27 for T
inserted A at 22, before A
inserted T at 190, before G
swapped C at 195 for C
inserted A at 274, before G
1: AAGACCGATG TGTAGGTCTC GAAACATTCC TGGGGTAGCT CAGCTTGGGG
51: GTTGACCCTG TCTTGCTCCC ATGAACTGAG GATTTGGAAA TAACGCTTAT
101: AACTGCGGGG GATTGATATG GGACATTGTT GCTGTAGGGC TTCGGCGTGC
151: TTAGAAACAA GAGAACACAA TTTCGATAGA CCAGGTTTCT GTCCCGCTAC
201: GAGTGATAGT AGCGCGTTAG GATTAATAAT CAGGGAGAGC ATTAAACATT
251: CTAAAAACTG ACATTCCCGA GGTAGGAACC CGAGTTGATA ACGAGTATGC
301: TCTGAAAAAT TAATTGATTG ATCCGCGACA CTAATCACAC CGTCTTCGCC
351: GTTGTAATGC ATGCTGGCTT AGCATCCGGA TGCTCTTCTA CCGATCTTAA
401: GGCGCGCACT CCCCAAGGAG CATAGAAGCA TCCCCGGCCC TCGACAGAGT
451: CTCCCAGTGT AAGTGTCTTT ATCCAAAATC
Base counts: A:128, C:110, G:119, T:123, total:480
</pre>
=={{header|Python}}==
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