Perl regex k-mers function to c# analog

Question

There is a perl function that finds and prints all the overlapping k-mers of the input string.

#!/pkg/bin/perl -w

print "Input the string\n";
$dna = <>;
chomp $dna;
print "Input the length of the window\n"; 
$k = <>;
chomp $k;

while (length($dna) >= $k) {
$dna =~ m/(.{$k})/; 
print "$1 \n";
$dna = substr($dna, 1, length($dna) -1);;
}

I would like to make it a function so instead of a string it receives a list of strings and get all k-mers, so I am trying something like:

//first try with defined string and k to see if it works
string dna="ATTTGGC\nTGCCTTA\nCGGTATC\nGAAAATT";
dna.Replace("\n", "");  //instead of chomp
int k=3;
while(dna.Length  >= k){
  //here I do not know how to traslate $dna =~ m/(.{$k})/; 
  //print "$1 \n";
  //$dna = substr($dna, 1, length($dna) -1);;
}

what would be the best way to translate that function from perl to c#?

Tim S. · Accepted Answer · 2013-12-04 16:49:21Z

1

You should use Regex's Match method.

string dna = "ATTTGGC\nTGCCTTA\nCGGTATC\nGAAAATT";
dna = dna.Replace("\n", "");
int k = 3;
var r = new Regex(@"(.{" + k + @"})");
while (dna.Length >= k)
{
    Match m = r.Match(dna);
    Console.WriteLine(m.ToString());
    dna = dna.Substring(1);
}

Note that since strings in C# are immutable, you have to do dna = dna.Replace... for it to have an effect.

This prints ATT, TTT, TTG, etc. just like your Perl method. This could be rewritten as a simpler loop and Substring, and avoid regex entirely.

answered Dec 4, 2013 at 16:49

Tim S.

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2 Comments

edgarmtze Over a year ago

So it would be fast to do it without regex? That is true for every string length right?. What would be the best way to do it int k=3; for(int i=0; i< dna.Length+1; i+=k){ ... } ?

Tim S. Over a year ago

i would only increment by 1, since that's how far you want to move the starting place by, so use i++ (k comes into play in knowing how long each substring should be and in knowing the max i to go to); and you're going too far, it should be some amount less than dna.Length. You're on the right track to write and debug it yourself, though.

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