Anonymous user
Bioinformatics/Sequence mutation: Difference between revisions
→{{header|zkl}}: added code
m (→{{header|Python}}: add zkl header) |
(→{{header|zkl}}: added code) |
||
Line 327:
=={{header|zkl}}==
<lang zkl>var [const] bases="ACGT", lbases=bases.toLower();
<lang zkl></lang>▼
dna:=(190).pump(Data().howza(3),(0).random.fp(0,4),bases.get); // bucket of bytes
foreach s,m in (T("Original","Mutated").zip(T(True,False))){
println("\n",s," DNA strand:"); dnaPP(dna);
println("Base Counts: ", dna.len()," : ",
dna.text.toUpper().counts() // ("A",5, "C",10, ...)
.pump(String,Void.Read,"%s(%d) ".fmt));
if(m) mutate(dna,10,True);
}
fcn mutate(dna,count=1,verbose=False){
if(verbose) println("Mutating:");
do(count){
n,rb := (0).random(dna.len()), lbases[(0).random(4)];
switch( (0).random(3) ){
case(0){ if(verbose) println("Change[%d] '%s' to '%s'".fmt(n,dna.charAt(n),rb));
dna[n]=rb;
}
case(1){ if(verbose) println("Delete[%d] '%s'".fmt(n,dna.charAt(n)));
dna.del(n);
}
else{ if(verbose) println("Insert[%d] '%s'".fmt(n,rb));
dna.insert(n,rb);
}
}
}
}
fcn dnaPP(dna,N=50){
[0..*,50].zipWith(fcn(n,bases){ println("%6d: %s".fmt(n,bases.concat())) },
dna.walker().walk.fp(50)).pump(Void); // .pump forces the iterator
{{out}}
<pre>
Original DNA strand:
0: AACGACAGGTTCTCGATGCGTGTCTTCACACATGTGGAGTCGCCAAGGAT
50: TGTTGATCAATGCGTAAACGTCTCCACGGGATACACGGGCAGCTTGCGGT
100: GACGAGTGCGGACCACCAAAAAAGGTGGGATCCACGTTGAGGAGCCTCAC
150: TACCTACGGCGTGATATGGCGGCAGGAGTCAAAAACTGCT
Base Counts: 190 : A(49) C(46) G(57) T(38)
Mutating:
Insert[123] 'c'
Insert[69] 't'
Delete[5] 'C'
Delete[147] 'T'
Change[167] 'G' to 't'
Change[153] 'C' to 'c'
Insert[151] 't'
Insert[156] 't'
Delete[150] 'T'
Change[102] 'C' to 'g'
Mutated DNA strand:
0: AACGAAGGTTCTCGATGCGTGTCTTCACACATGTGGAGTCGCCAAGGATT
50: GTTGATCAATGCGTAAACtGTCTCCACGGGATACACGGGCAGCTTGCGGT
100: GAgGAGTGCGGACCACCAAAAAAcGGTGGGATCCACGTTGAGGAGCCCAC
150: tACcTtACGGCGTGATATtGCGGCAGGAGTCAAAAACTGCT
Base Counts: 191 : A(49) C(45) G(57) T(40)
</pre>
| |||