Example Program
File Format I/O
Accessing sequence data in files.
File "file_format.cpp"
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 |
8 | using namespace seqan;
9 |
10 | int 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 |

See
write, read, readMeta, File Reader String
SeqAn - Sequence Analysis Library - www.seqan.de

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