getAlleleSequences

Description: Returns all allele sequences defined for a locus.

Arguments

• database (string)
• locus (string)

Sample Perl code

#!/usr/bin/perl
#Written by Keith Jolley

use SOAP::Lite;
use strict;
use warnings;

#####Sample arguments#########
my $database = 'neisseria';
my $locus = 'abcZ';
##############################

my $soap = SOAP::Lite
    -> uri('http://pubmlst.org/MLST')
    -> proxy('http://pubmlst.org/cgi-bin/mlstdbnet/mlstFetch.pl');
my $soapResponse = $soap->getAlleleSequences($database,$locus);
unless ($soapResponse->fault){
    for my $t ($soapResponse->valueof('//allele')) {
	print ">$locus-" .$t->{'id'} . "\n" . $t->{'sequence'} . "\n";
    }
} else {
    print join ', ',$soapResponse->faultcode,$soapResponse->faultstring;
}

Sample Java code

package org.pubmlst.mlstSOAP;

import org.apache.axis.client.Call;
import org.apache.axis.client.Service;
import javax.xml.namespace.QName;
import java.util.Vector;

public class GetAlleleSequences {

    public static void main(String[] args) {
	//Sample arguments////////////////
	String database = "neisseria";
	String locus = "abcZ";
	//////////////////////////////////
	try {
	    String endpoint = "http://pubmlst.org/cgi-bin/mlstdbnet/mlstFetch.pl";
	    Service service = new Service();
	    Call call = (Call) service.createCall();
	    call.setTargetEndpointAddress(new java.net.URL(endpoint));
	    call.setOperationName(new QName("http://pubmlst.org/MLST/",
					    "getAlleleSequences"));
	    call.addParameter("database",org.apache.axis.Constants.XSD_STRING,
			      javax.xml.rpc.ParameterMode.IN);
	    call.addParameter("locus",org.apache.axis.Constants.XSD_STRING,
			      javax.xml.rpc.ParameterMode.IN);
	    call.setReturnType(org.apache.axis.Constants.SOAP_VECTOR);
	    Vector ret = (Vector) call.invoke(new Object[] { database,locus });
	    for (int i=0; i<ret.size(); i++){
		Vector allele = (Vector)ret.get(i);
		System.out.println(">" + locus + "-" + allele.get(0));
		System.out.println(allele.get(1));
	    }
	} catch (Exception e) {
	    System.err.println(e.toString());
	}
    }
}