/usr/share/doc/libbiojava-java-demos/examples/seq/ReverseComplement.java is in libbiojava-java-demos 1:1.7.1-5.
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The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 | /*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package seq;
import java.io.*;
import org.biojava.bio.seq.SequenceTools;
import org.biojavax.Namespace;
import org.biojavax.RichObjectFactory;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.seq.RichSequenceIterator;
/**
* Demo of reverse complementing a fasta DNA file
* @author Matthew Pocock
* @author Mark Schreiber
*/
public class ReverseComplement {
/**
* Run the program
* @param args a dna fasta file
*/
public static void main(String[] args)
throws Exception {
if(args.length < 1) {
System.err.println("Use: seq.ReverseComplement inFile");
System.exit(1);
}
BufferedReader seqIn = new BufferedReader(
new FileReader(
new File(args[0])
)
);
OutputStream seqOut = System.out;
Namespace ns = RichObjectFactory.getDefaultNamespace();
for(RichSequenceIterator si = RichSequence.IOTools.readFastaDNA(seqIn, ns);
si.hasNext(); ) {
RichSequence seq = si.nextRichSequence();
RichSequence rev = RichSequence.Tools.enrich(SequenceTools.reverseComplement(seq));
RichSequence.IOTools.writeFasta(seqOut, rev, ns);
}
}
}
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