Example Program
File Format I/O
Accessing sequence data in files.
A tutorial about the use of files and file formats.
1#include <iostream>
2#include <fstream>
3#include <cstdio>
4
5#include <seqan/sequence.h>
6#include <seqan/file.h>
7
8using namespace seqan;
9
10int main()
11{
Open a standard library stream for binary write. You can use both C++ iostreams or old style FILE pointer. The file format is Fasta.
12    std::FILE * fl = std::fopen("testfile.fa", "wb");
13    write(fl, "aacagtattagaccactaggaccct", "a test file", Fasta());
14    close (fl);
Read a fasta file.
15    std::fstream fstrm;
16    fstrm.open("testfile.fa", std::ios_base::in | std::ios_base::binary);
17    String<char> fasta_tag;
18    String<Dna> fasta_seq;
Read the meta-information.
19    readMeta(fstrm, fasta_tag, Fasta());
20    std::cout << fasta_tag << "\n";    //prints "a test file"
Read the sequence.
21    read(fstrm, fasta_seq, Fasta());
22    std::cout << fasta_seq << "\n";    //prints the sequence
23    fstrm.close();
Open a file using a file reader string.
24    String<Dna, FileReader<Fasta> > fr("testfile.fa");
25    std::cout << fr << "\n";            //prints the sequence
26    return 0;
27}
28
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