[Biojava-l] A Exception Has Occurred During Parsing.

[mark.schreiber at novartis.com]

Hi -

Judging by the sporadic nature of the bug and the error report I think you 
are correct that there is an I/O problem. I think you are not getting back 
a Genbank format object but probably an error message from NCBI or a time 
out return or similar.

It would be useful if the NCBIGenbankSequenceFetcher could be modified to 
optionally log the response to the URL.

Best regards,

- Mark

biojava-l-bounces at lists.open-bio.org wrote on 12/11/2009 07:36:46 PM:

> 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
> >> biojava-l at biojava.org 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
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >> 
> > --
> > Richard Holland, BSc MBCS
> > Operations and Delivery Director, Eagle Genomics Ltd
> > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> > http://www.eaglegenomics.com/
> >
> >
> > 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

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