How to Read a Fasta File with Biojava3

```java import; import; import java.util.LinkedHashMap; import java.util.Map.Entry;

import org.biojava.nbio.core.sequence.ProteinSequence; import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet; import; import; import; import;

public class FastaOpen {

   public static void main(String[] args) throws Exception{
        * Method 1: With the FastaReaderHelper
       //Try with the FastaReaderHelper
       LinkedHashMap<String, ProteinSequence> a = FastaReaderHelper.readFastaProteinSequence(new File(args[0]));
       //FastaReaderHelper.readFastaDNASequence for DNA sequences
       for (  Entry<String, ProteinSequence> entry : a.entrySet() ) {
           System.out.println( entry.getValue().getOriginalHeader() + "=" + entry.getValue().getSequenceAsString() );
        * Method 2: With the FastaReader Object 
       //Try reading with the FastaReader
       FileInputStream inStream = new FileInputStream( args[0] );
       FastaReader<ProteinSequence,AminoAcidCompound> fastaReader = 
           new FastaReader<ProteinSequence,AminoAcidCompound>(
                   new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(), 
                   new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
       LinkedHashMap<String, ProteinSequence> b = fastaReader.process();
       for (  Entry<String, ProteinSequence> entry : b.entrySet() ) {
           System.out.println( entry.getValue().getOriginalHeader() + "=" + entry.getValue().getSequenceAsString() );



How to Write a Fasta File with Biojava3

Fasta files can be written with FastaWriterHelper. The description line is determined by GenericFastaHeaderFormat.getHeader, which first attempts to write the OriginalHeader from the sequence, and otherwise writes the accessionID. If neither of these properties are defined, the description will be blank and it will not be possible to read the file into a HashMap, as with the FastaReader and FastaReaderHelper, above. These properties can be set with Sequence.setOriginalHeader and Sequence.setAccession.