Read SequenceIO

Reading and writing files with ReadSequence data

Introduction

Files with ReadSequence data can be read with a class implementing the ReadSequenceReader interface and written with a class implementing the ReadSequenceWriter interface. Currently the Fasta format and TFQ (see Read Sequence) are handled in Eoulsan.

Read a FASTQ file

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

ReadSequenceReader reader = new FastqReader(new File("in.fastq");

for (ReadSequence read : reader) {
  System.out.println(read);
}
// Throw an exception if an error has occurred while reading data
reader.throwException();

reader.close();

Read a TFQ file

The reading of a TFQ works like reading a FASTQ file:

ReadSequenceReader reader = new TFQReader(new File("in.tfq");

for (ReadSequence read : reader) {
  System.out.println(read);
}

reader.close();

Write a FASTQ file

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

ReadSequence read1 = new Sequence(1, "seq1", "AAAATTTT", "!''*((((");
ReadSequence read2 = new Sequence(2, "seq2", "GGGGCCCC", "***+))%%");

ReadSequenceWriter writer = new FastqWriter(new File("out.fasta"); 

writer.write(read1);
writer.write(read2);

writer.close();

Write a TFQ file

The writing of a TFQ works like writing a FASTQ file:

ReadSequence read1 = new Sequence(1, "seq1", "AAAATTTT", "!''*((((");
ReadSequence read2 = new Sequence(2, "seq2", "GGGGCCCC", "***+))%%");

ReadSequenceWriter writer = new TFQWriter(new File("out.fasta"); 

writer.write(read1);
writer.write(read2);

writer.close();