How Do I Print A Sequence in Fasta Format?

FASTA format is a fairly standard bioinformatics output that is convenient and easy to read. BioJava has a tools class called IOTools that provides static convenience methods to perform a number of common bioinformatics IO tasks. The follwing snippets demonstrate how to print a Sequence or even a whole SequenceDB in FASTA format to an OutputStream like System.out. All of the WriteXX methods from IOTools take an OutputStream as an argument. In this way you can pipe the newly formatted sequence to a file or another method or STDOUT, STDERR etc.

IOTools is in the package

Printing a SequenceDB with an Iterator

```java private static void printSequenceDB() {

       SequenceDB db = new HashSequenceDB();       
       Sequence dna1;
       Sequence dna2;
       try {
           dna1 = DNATools.createDNASequence("atgctgtgg", "dna_1");
           dna2 = DNATools.createDNASequence("atgctgctt", "dna_2");
           RichSequence.IOTools.writeFasta(System.out, db.sequenceIterator(), null);
       } catch (Exception e) {

### Printing a Single Sequence


`     /*`  
`      * SeqIOTools also has a method that takes a single sequence so you don't`  
`      * have to make a SequenceDB`  
`      */`  
`       private static void printSingleSequence(){`  
`       Sequence dna;`  
`       try {`  
`           dna = DNATools.createDNASequence("atgctg", "dna_1");`  
`           RichSequence.IOTools.writeFasta(System.out, dna, null);`  
`       } catch (IllegalSymbolException e) {`  
`           e.printStackTrace();`  
`       } catch (IOException e) {`  
`           e.printStackTrace();`  
`       }       `  
`   }`