source code
/* The Computer Language Benchmarks Game
http://benchmarksgame.alioth.debian.org/
*
* regex-dna program contributed by Isaac Gouy
* converted from regex-dna program
*
*/
using System;
using System.Text.RegularExpressions;
class regexredux
{
static void Main(string[] args){
// read FASTA sequence
String sequence = Console.In.ReadToEnd();
int initialLength = sequence.Length;
// remove FASTA sequence descriptions and new-lines
Regex r = new Regex(">.*\n|\n", RegexOptions.Compiled);
sequence = r.Replace(sequence,"");
int codeLength = sequence.Length;
// regex match
string[] variants = {
"agggtaaa|tttaccct"
,"[cgt]gggtaaa|tttaccc[acg]"
,"a[act]ggtaaa|tttacc[agt]t"
,"ag[act]gtaaa|tttac[agt]ct"
,"agg[act]taaa|ttta[agt]cct"
,"aggg[acg]aaa|ttt[cgt]ccct"
,"agggt[cgt]aa|tt[acg]accct"
,"agggta[cgt]a|t[acg]taccct"
,"agggtaa[cgt]|[acg]ttaccct"
};
int count;
foreach (string v in variants){
count = 0;
r = new Regex(v, RegexOptions.Compiled);
for (Match m = r.Match(sequence); m.Success; m = m.NextMatch()) count++;
Console.WriteLine("{0} {1}", v, count);
}
// regex substitution
IUB[] codes = {
new IUB("tHa[Nt]", "<4>")
,new IUB("aND|caN|Ha[DS]|WaS", "<3>")
,new IUB("a[NSt]|BY", "<2>")
,new IUB("<[^>]*>", "|")
,new IUB("\\|[^|][^|]*\\|" , "-")
};
foreach (IUB iub in codes) {
r = new Regex(iub.code, RegexOptions.Compiled);
sequence = r.Replace(sequence,iub.alternatives);
}
Console.WriteLine("\n{0}\n{1}\n{2}",
initialLength, codeLength, sequence.Length);
}
struct IUB
{
public string code;
public string alternatives;
public IUB(string code, string alternatives) {
this.code = code;
this.alternatives = alternatives;
}
}
}