SequenceIO

Reading and writing files with Sequence data

WARNING: This documentation is outdated and will soon be updated.

Introduction

Files with Sequence data can be read with a class implementing the SequenceReader interface and written with a class implementing the SequenceWriter interface. Currently only the Fasta format is handled in Eoulsan.

Read a FASTA file

As the SequenceReader extends the Iterable and Iterator interface, it is quite easy to read the entries of a FASTA using a for loop:

SequenceReader reader = new FastaReader(new File("in.fasta");

for (Sequence seq : reader) {
  System.out.println(seq);
}
// Throw an exception if an error has occured while reading data
reader.throwException();

reader.close();

Write a FASTA file

Writing a FASTA file is also very easy, you just have to create the FastaWriter and call the write(Sequence) method to add the sequences to the file. Don't forget to close the file after adding the last sequence of the file.

Sequence seq1 = new Sequence(1, "seq1", "AAAATTTT");
Sequence seq2 = new Sequence(2, "seq2", "GGGGCCCC");

SequenceWriter writer = new FastaWriter(new File("out.fasta"); 

writer.write(seq1);
writer.write(seq2);

writer.close();