[Biojava-l] sort fasta file
xyz
mitlox at op.pl
Sat Mar 20 10:17:17 UTC 2010
Hello,
I would like to sort multiple fasta file depends on the sequence length,
ie. from the read with longest sequence to the read with the shortest
sequence.
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import org.biojava.bio.BioException;
import org.biojavax.SimpleNamespace;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.seq.RichSequenceIterator;
public class SortFasta {
public static void main(String[] args) throws FileNotFoundException,
BioException {
BufferedReader br = new BufferedReader(new
FileReader("sortfasta.fasta")); SimpleNamespace ns = new
SimpleNamespace("biojava");
RichSequenceIterator rsi = RichSequence.IOTools.readFasta(br, null,
ns);
while (rsi.hasNext()) {
RichSequence rs = rsi.nextRichSequence();
System.out.println(rs.getName());
System.out.println(rs.seqString());
}
}
}
I have tried to do it, but I do not how to continue.
Thank you in advance.
Best regards,
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