你可以试试,
#include <iostream>
#include <seqan/sequence.h> // CharString, ...
#include <seqan/find.h>
#include <seqan/stream.h>
using namespace seqan;
typedef Iterator<StringSet<Dna5String> >::Type TStringSetIterator;
int main(int, char const **)
{
StringSet<Dna5String> seqs;
Dna5String seq1 =
"TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG"
"TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG"
"AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC"
"GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTCATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT"
"CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA"
"CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT"
"CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG";
Dna5String seq2 =
"ACCGACGATTAGCTTTGTCCGAGTTACAACGGTTCAATAATACAAAGGATGGCATAAACCCATTTGTGTGAA"
"AGTGCCCATCACATTATGATTCTGTCTACTATGGTTAATTCCCAATATACTCTCGAAAAGAGGGTATGCTCC"
"CACGGCCATTTACGTCACTAAAAGATAAGATTGCTCAAANNNNNNNNNACTGCCAACTTGCTGGTAGCTTCA"
"GGGGTTGTCCACAGCGGGGGGTCGTATGCCTTTGTGGTATACCTTACTAGCCGCGCCATGGTGCCTAAGAAT"
"GAAGTAAAACAATTGATGTGAGACTCGACAGCCAGGCTTCGCGCTAAGGACGCAAAGAAATTCCCTACATCA"
"GACGGCCGCGNNNAACGATGCTATCGGTTAGGACATTGTGCCCTAGTATGTACATGCCTAATACAATTGGAT"
"CAAACGTTATTCCCACACACGGGTAGAAGAACNNNNATTACCCGTAGGCACTCCCCGATTCAAGTAGCCGCG";
clear(seqs);
appendValue(seqs, seq1);
appendValue(seqs, seq2);
Pattern<Dna5String, Simple> pattern(Dna5String("GAATTC"));
//For each sequence in seqs
for (TStringSetIterator it = begin(seqs); it != end(seqs); ++it)
{
std::cout << *it << std::endl;
//I create a finder for each sequence in seqs
Finder<Dna5String> finder(*it);
if (find(finder, pattern)){
std::cout << '[' << beginPosition(finder) << ',' << endPosition(finder)
<< ")\t" << infix(finder) << std::endl;
}else{
std::cout << "No match!" << std::endl;
}
}
return 0;
}
你得到:
TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTGTTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACGAGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCACGGTGCCACATGTCTTATCTATTCAGGGATCAGAATTCATTCAGGAAATCAGGAGATGCTACACTTGGGTTATCGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACACGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGATCGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG
[247,253) GAATTC
ACCGACGATTAGCTTTGTCCGAGTTACAACGGTTCAATAATACAAAGGATGGCATAAACCCATTTGTGTGAAAGTGCCCATCACATTATGATTCTGTCTACTATGGTTAATTCCCAATATACTCTCGAAAAGAGGGTATGCTCCCACGGCCATTTACGTCACTAAAAGATAAGATTGCTCAAANNNNNNNNNACTGCCAACTTGCTGGTAGCTTCAGGGGTTGTCCACAGCGGGGGGTCGTATGCCTTTGTGGTATACCTTACTAGCCGCGCCATGGTGCCTAAGAATGAAGTAAAACAATTGATGTGAGACTCGACAGCCAGGCTTCGCGCTAAGGACGCAAAGAAATTCCCTACATCAGACGGCCGCGNNNAACGATGCTATCGGTTAGGACATTGTGCCCTAGTATGTACATGCCTAATACAATTGGATCAAACGTTATTCCCACACACGGGTAGAAGAACNNNNATTACCCGTAGGCACTCCCCGATTCAAGTAGCCGCG
不匹配!
编辑,我希望这对你有帮助
....
#include <seqan/index.h>
....
Pattern<Dna5String> pattern(Dna5String("GAATTC"));
Index< StringSet<Dna5String > > myIndex(seqs);
Finder< Index<StringSet<Dna5String > > > finder(myIndex);
while (find(finder, pattern)){
std::cout << '[' << beginPosition(finder) << ',' << endPosition(finder)
<< ")\t" << infix(finder) << std::endl;
}
....
你得到,
[< 0 , 247 >,< 0 , 253 >) GAATTC