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Bugfix in hmmer web service #640

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Merged
andreasprlic merged 1 commit into from
Mar 2, 2017
Merged

Bugfix in hmmer web service #640

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41 changes: 15 additions & 26 deletions biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,8 @@
import net.sf.json.JSONArray;
import net.sf.json.JSONObject;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.*;
import java.net.HttpURLConnection;
Expand All @@ -31,14 +33,17 @@
import java.util.TreeSet;


/** Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.
/**
* Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.
*
* @author Andreas Prlic
* @since 3.0.3
*/
public class RemoteHmmerScan implements HmmerScan {

public static String HMMER_SERVICE = "http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan";
private static final Logger LOGGER = LoggerFactory.getLogger(RemoteHmmerScan.class);

public static final String HMMER_SERVICE = "http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan";

public RemoteHmmerScan(){

Expand All @@ -54,7 +59,8 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence) throws IOException

}

/** Scans a protein sequence for Pfam profile matches.
/**
* Scans a protein sequence for Pfam profile matches.
*
* @param sequence
* @param serviceLocation
Expand All @@ -68,7 +74,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
postContent.append("hmmdb=pfam");


// by default hmmscan runs with the HMMER3 cut_ga parameter enabled, the "gathering freshold", which depends on
// by default hmmscan runs with the HMMER3 cut_ga parameter enabled, the "gathering threshold", which depends on
// the cutoffs defined in the underlying HMM files.
// to request a different cutoff by e-value this could be enabled:
//postContent.append("&E=1");
Expand All @@ -86,7 +92,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
connection.setRequestMethod("POST");
connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");

connection.setRequestProperty("Accept:","application/json");
connection.setRequestProperty("Accept","application/json");

connection.setRequestProperty("Content-Length", "" +
Integer.toString(postContent.toString().getBytes().length));
Expand All @@ -99,13 +105,12 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
wr.close ();


// //Now get the redirect URL
//Now get the redirect URL
URL respUrl = new URL( connection.getHeaderField( "Location" ));

int responseCode = connection.getResponseCode();
if ( responseCode == 500){
System.err.println("something went wrong!" + serviceLocation);
System.err.println(connection.getResponseMessage());
LOGGER.warn("Got 500 response code for URL {}. Response message: {}.", serviceLocation, connection.getResponseMessage());
}

HttpURLConnection connection2 = (HttpURLConnection) respUrl.openConnection();
Expand All @@ -122,7 +127,6 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation

StringBuffer result = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
//System.out.println(inputLine);
result.append(inputLine);
}

Expand All @@ -141,7 +145,6 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation

for(int i =0 ; i < hits.size() ; i++){
JSONObject hit = hits.getJSONObject(i);
//System.out.println("hit: "+ hit);

HmmerResult hmmResult = new HmmerResult();

Expand Down Expand Up @@ -170,35 +173,21 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
for ( int j= 0 ; j < hmmdomains.size() ; j++){
JSONObject d = hmmdomains.getJSONObject(j);
//System.out.println(d);
Integer is_included = getInteger(d.get("is_included"));
if ( is_included == 0) {
// System.out.println(" excluding: " + d.get("alihmmdesc") + " " + d.get("alihmmname") + " " +
// hit.get("evalue") + " " +
// d.get("alisqfrom") + " " +
// d.get("alisqto"));
continue;
}


// this filters out multiple hits to the same clan
Integer outcompeted = getInteger(d.get("outcompeted"));
if ( outcompeted != null && outcompeted == 1) {
// System.out.println(" outcompeted: " + d.get("alihmmdesc") + " " + d.get("alihmmname")+ " " +
// hit.get("evalue") + " " +
// d.get("alisqfrom") + " " +
// d.get("alisqto")
// );
continue;
}

Integer significant = getInteger(d.get("significant"));

if ( significant != 1) {
// System.out.println(" not significant: " + d.get("alihmmdesc") + " " + d.get("alihmmname")+ " " +
// hit.get("evalue") + " " +
// d.get("alisqfrom") + " " +
// d.get("alisqto"));
continue;
}

Expand All @@ -224,8 +213,8 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation

results.add(hmmResult);
}
} catch (Exception e){
e.printStackTrace();
} catch (NumberFormatException e){
LOGGER.warn("Could not parse number in Hmmer web service json response: {}", e.getMessage());
}

return results;
Expand Down
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