Read GenBank file

Value

Script

import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.io.SeqIOTools;
import org.biojava.bio.seq.io.agave.AgaveWriter;

BufferedReader getReader (String fileUrl) throws IOException {
		InputStreamReader reader;
		try {
			reader = new FileReader(fileUrl);
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			reader = new InputStreamReader (url.openStream());
		}
		return new BufferedReader(reader);
	}
	
BufferedReader br  = getReader(fileUrl);

// read the GenBank File
SequenceIterator sequences = SeqIOTools.readGenbank(br);

// iterate through the sequences
ByteArrayOutputStream os = new ByteArrayOutputStream();
StringBuffer sb = new StringBuffer();
AgaveWriter writer = new AgaveWriter();
PrintStream ps = new PrintStream(os);

while (sequences.hasNext()) {
	Sequence seq = sequences.nextSequence();
	writer.writeSequence(seq, ps);
	sb.append(os.toString());
}

genbankdata = sb.toString()