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#include <iostream>
#include <fstream>
#include <seqan/index.h>
#include <seqan/statistics.h>
#include <seqan/seq_io.h>
using namespace seqan;
int main()
{
// Build path to background FASTA file.
CharString bgPath = getAbsolutePath("/demos/statistics/background.fa");
// Read the background from a file into X.
StringSet<DnaString> X;
SeqFileIn seqFile;
if (!open(seqFile, toCString(bgPath)))
{
std::cerr << "ERROR: Could not open " << bgPath << "\n";
return 1;
}
StringSet<CharString> ids; // will be ignored
readRecords(ids, X, seqFile);
// Create MarkovModel of order 3 from the background.
MarkovModel<Dna> mm(3);
buildMarkovModel(mm, X);
// Build set of words that we want to compute the zscore of.
StringSet<DnaString> W;
appendValue(W, "CCCAAAGC");
appendValue(W, "CCCAAAGTAAATT");
// Compute and print zscore.
std::cout << "zscore: " << zscore(W, X, mm, AhoCorasick()) << "\n";
// //TODO his path has to be set explicitely when calling the demo
// FILE *fd = fopen("projects/library/demos/zscore_human_mm.3","r");
// read(fd, mm);
// fclose(fd);
//std::cout << zscore(W, X, mm, WuManber()) << std::endl;
return 0;
}
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