I created a new class NCBIGenbankSequenceFetcher.java which extends
GenbankRichSequenceDB and overrid the "getAddress(String id)" to limit
the sequence for an id (seq_start and seq_stop).
public class NCBIGenbankSequenceFetcher extends GenbankRichSequenceDB{
private String seq_start;
private String seq_stop;
private String strand="1";//1=plus, 2=minus
public NCBIGenbankSequenceFetcher() {
}
public NCBIGenbankSequenceFetcher(String seq_start, String seq_stop) {
this.seq_start = seq_start;
this.seq_stop = seq_stop;
}
public NCBIGenbankSequenceFetcher(String seq_start, String
seq_stop,String strand) {
this.seq_start = seq_start;
this.seq_stop = seq_stop;
this.strand = strand;
}
@Override
protected URL getAddress(String id) throws MalformedURLException {
FetchURL seqURL = new FetchURL("Genbank", "text");
String baseurl = seqURL.getbaseURL();
String db = seqURL.getDB();
String url = baseurl+db+"&id="+id+"&rettype=gb";
if(seq_start != null && seq_stop != null){
url
+="&seq_start="+seq_start+"&seq_stop="+seq_stop+"&strand="+strand;
}
return new URL(url);
}
}
From an other class, i create an instance of this class and then call
its "getRichSequence(id)" method. (Not the same, but similar)
for(String gi:ids){ // ids is a list<string>
seq = new NCBIGenbankSequenceFetcher(seq_start,
seq_stop,strand).getRichSequence(gi);
}
What i found later is that it randomly throws the exception, not by any
particular sequence. So my guess an io error, which arises during the
data streaming from server.
ilhami visne.
On 12/11/2009 10:59 AM, Richard Holland wrote:
Hello. Could you also post the relevant parts of your code that you are running
when this exception happens?
cheers,
Richard
On 11 Dec 2009, at 00:46, Ilhami Visne wrote:
Hi,
I'm following the suggestion "Please submit the details that follow to
[email protected] or post a bug report to http://bugzilla.open-bio.org/";
.
The sequence of concerns is at
http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=39645757&rettype=gb&seq_start=1353&seq_stop=2128&strand=1
Format_object=org.biojavax.bio.seq.io.GenbankFormat
Accession=null
Id=null
Comments=Bad section
Parse_block=
Stack trace follows ....
at
org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:603)
at
org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:278)
at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
... 8 more
Caused by: java.lang.NullPointerException
at
org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:593)
... 10 more
org.biojava.bio.BioException: IO failure whilst reading from Genbank
Any quick fix,patch?
thanks.
Ilhami Visne
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--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/
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