Files

File Input/Output.

Contents

1 Raw Data

SeqAn supports the input and output of files in different file formats. The most simple file format is Raw that is used to load a file "as is" into a string or vice versa.

//Loading.
::std::fstream fstrm;
fstrm.open("input.txt", ::std::ios_base::in | ::std::ios_base::binary);

String<char> str;
read(fstrm, str, Raw());
::std::cout << str << ::std::endl;
fstrm.close();

In this example, the tag Raw() can also be omitted, since Raw is the default file format. Instead of using read and write to read and write raw data, one can also use the operators << and >>.

Files can either be instances of a standard stream class, or a C-style stream (i.e. FILE *) or a SeqAn File object (see below). Note that the files should always be opened in binary mode.

2 File Formats for Bioinformatics

Apart from Raw, SeqAn offers other file formats relevant in bioinformatics such as Fasta, EMBL, or Genbank. These file formats consist of one or more data records. Multiple records in a file can be loaded by iteratively calling the function read.

::std::fstream fstrm;
fstrm.open("est.fasta", ::std::ios_base::in | ::std::ios_base::binary);
String<Dna> est;
while (! fstrm.eof()) {
read(fstrm, est, Fasta());
::std::cout << est << ::std::endl;
}

The function goNext skips the current record and proceeds to the next record.

Each record contains a piece of data (i.e. a sequence or an alignment) and optional some additional metadata. One can load these metadata before loading the actual data using readMeta. The function fills a string with the unparsed metadata.

::std::fstream fstrm;
fstrm.open("est.fasta", ::std::ios_base::in | ::std::ios_base::binary);
String<Dna> est;
String<char> meta;
while (! fstrm.eof())
{
readMeta(fstrm, meta, Fasta());
::std::cout << meta << ::std::endl;
read(fstrm, est, Fasta());
::std::cout << est << ::std::endl;
}

write is used to write a record into a file. Depending on the file format, a suitable metadata string must be passed to write.

FILE * cstrm = fopen("genomic_data.fa", "w");
write(cstrm, "acgt", "the metadata", Fasta());
fclose(cstrm);

This code creates the following file "genomic_data.fa".

>the metadata
ACGT

3 File Reader Strings

The easiest way for a read-only access of sequence data stored in a file is a file reader string. A file reader string implements the container concept, i.e. it implements common functions like length or begin. It has minimal memory consumption, because each part of the sequence data is not loaded before it is needed.

String<Dna, FileReader<Fasta> > fr("ests.fa");
//Print the length of the first sequence.
::std::cout << length(fr);

The constructor of the file reader string can also take a file from which the sequences will be loaded. For example, the following code will read the second sequence in the file:

FILE * cstrm = fopen("est.fasta", "r");
goNext(cstrm, Fasta());
//Read the meta data of the second record.
String<char> meta_data;
readMeta(cstrm, meta_data, Fasta());
::std::cout << meta_data << ::std::endl;
//Read the sequence data of the second record.
String<Dna, FileReader<Fasta> > fr(cstrm);
::std::cout << fr << ::std::endl;
fclose(cstrm);

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