// code to read the fasta file
import java.io.*;
import java.util.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;
import org.biojavax.bio.seq.RichSequenceIterator;
import org.biojavax.bio.seq.io.FastaHeader;
import static org.biojavax.bio.seq.RichSequence.IOTools;
public class ReadFasta {
/**
* The program takes two args: the first is the file name of the Fasta file.
* The second is the name of the Alphabet. Acceptable names are DNA RNA or PROTEIN.
*/
public static void main(String[] args) {
try {
//setup file input
String filename = args[0];
BufferedInputStream is =
new BufferedInputStream(new FileInputStream(filename));
//get the appropriate Alphabet
Alphabet alpha = AlphabetManager.alphabetForName(args[1]);
//get a SequenceDB of all sequences in the file
SequenceDB db = org.biojavax.bio.seq.RichSequence.IOTools.readFasta(is, alpha);
//SequenceDB db = org.biojava.bio.seq.io.SeqIOTools.readFasta(is, alpha);
//org.biojavax.bio.seq.RichSequence.IOTools
}
catch (BioException ex) {
//not in fasta format or wrong alphabet
ex.printStackTrace();
}catch (NoSuchElementException ex) {
//no fasta sequences in the file
ex.printStackTrace();
}catch (FileNotFoundException ex) {
//problem reading file
ex.printStackTrace();
}
}
}
safee86 0 Newbie Poster
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