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HmmerDemo.java
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95 lines (74 loc) · 2.62 KB
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/*
* 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 demo;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
import org.biojava.nbio.ws.hmmer.HmmerDomain;
import org.biojava.nbio.ws.hmmer.HmmerResult;
import org.biojava.nbio.ws.hmmer.RemoteHmmerScan;
import java.util.SortedSet;
/**
* The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service
*
* @author Andreas Prlic
* @since 3.0.3
*/
public class HmmerDemo {
public static void main(String[] args) throws Exception {
// first we get a UniProt sequence
String uniProtID = "P08487";
ProteinSequence seq = getUniprot(uniProtID);
// now we submit this sequence to the Hmmer web site
RemoteHmmerScan hmmer = new RemoteHmmerScan();
SortedSet<HmmerResult> results = hmmer.scan(seq);
// and now let's print out the obtained annotations
System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s",
"Domain","ACC", "Start","End","eValue","Description"));
int counter = 0;
for (HmmerResult hmmerResult : results) {
//System.out.println(hmmerResult);
for ( HmmerDomain domain : hmmerResult.getDomains()) {
counter++;
System.out.println(String.format("%d\t%15s\t%10s\t%5d\t%5d\t%.2e\t%s",
counter,
hmmerResult.getName(), domain.getHmmAcc(),
domain.getSqFrom(),domain.getSqTo(),
domain.getEvalue(), hmmerResult.getDesc()
));
}
}
}
/**
* Fetch a protein sequence from the UniProt web site
*
* @param uniProtID
* @return a Protein Sequence
* @throws Exception
*/
private static ProteinSequence getUniprot(String uniProtID) throws Exception {
AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<>(uniProtID,set);
ProteinSequence seq = new ProteinSequence(uniprotSequence);
return seq;
}
}