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

[ilhami visne]

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/
>
>
>