[Biojava-l] A Exception Has Occurred During Parsing. (Ilhami Visne)
Deepak Sheoran
sheoran143 at gmail.com
Sun Dec 13 22:11:44 UTC 2009
Hi,
I am attaching a quick fix to solve you problem with this record. Please
have look on the attached .jpeg file to see the solution.
Thanks
Deepak Sheoran
> 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
>
>
>
> ------------------------------------------------------------------------
>
> Subject:
> Re: [Biojava-l] A Exception Has Occurred During Parsing.
> From:
> Richard Holland <holland at eaglegenomics.com>
> Date:
> Fri, 11 Dec 2009 09:59:34 +0000
> To:
> Ilhami Visne <ilhami.visne at gmail.com>
>
> To:
> Ilhami Visne <ilhami.visne at gmail.com>
> CC:
> biojava-l at lists.open-bio.org
>
>
> 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/
>
>
>
>
>
> ------------------------------------------------------------------------
>
> Subject:
> Re: [Biojava-l] Sequences as strings to RichSequence iterator
> From:
> Oliver Stolpe <oliver.stolpe at fu-berlin.de>
> Date:
> Fri, 11 Dec 2009 11:44:26 +0100
> To:
> Richard Holland <holland at eaglegenomics.com>
>
> To:
> Richard Holland <holland at eaglegenomics.com>
> CC:
> biojava-l at biojava.org
>
>
> Dear Richard,
>
> thank you for your answer. What you stated in your PSS is exactly what
> I want. It worked well with the ByteArrayOutputStream. Nevertheless I
> dont use it but write my own string by concatenating the names and
> sequences using String s = ">" + name + "\r\n" + sequence + "\r\n". I
> know its not the best way but this fasta format thing modified the
> input names too much that I would have had to much trouble getting the
> right information out of them.
>
> Best regards,
> Oliver
>
> Richard Holland schrieb:
>> PS. Spot the deliberate mistake in the hasNext() function... that
>> should be <, not <=!
>>
>> PPS. In your original email you stated you wanted to read your
>> sequences as Fasta. In Biojava, all sequences are RichSequences -
>> they have no format other than the object model of RichSequence
>> itself. Fasta only gets involved when you're reading from a Fasta
>> file, or writing to one. If you need to show the sequences as Fasta
>> in your user interface, you should consider using the FastaWriter
>> writeSequence() method with the PrintStream parameter and wiring in a
>> StringWriter to the PrintStream so that you can get a String
>> representation of a Fasta record.
>>
>> On 6 Dec 2009, at 15:41, Richard Holland wrote:
>>
>>
>>> I'm not sure what you're trying to do here - are you trying to
>>> represent your string array of sequences as a RichSequenceIterator,
>>> or are you trying to convert them into FASTA? I'll answer both
>>> anyway...:
>>>
>>> To convert your String[] of sequences into a RichSequenceIterator
>>> you need to create a new class that implements the
>>> RichSequenceIterator interface. You would probably write something
>>> like this (which I have not checked or compiled - so if it has bugs,
>>> sorry!):
>>>
>>> public class MyDNASeqIterator implements RichSequenceIterator {
>>> private final String[] sequences;
>>> private final int counter;
>>>
>>> public MyDNASeqIterator(String[] sequences) { this.sequences =
>>> sequences; this.counter = 0; }
>>>
>>> public hasNext() { return this.counter <=
>>> this.sequences.length;
>>> }
>>>
>>> public Sequence nextSequence() { return nextRichSequence(); }
>>>
>>> public BioEntry nextBioEntry() { return nextRichSequence(); }
>>>
>>> public RichSequence nextRichSequence() {
>>> String seqName = "MySeq"+this.counter;
>>> return RichSequence.Tools.createRichSequence(seqName,
>>> this.sequences[this.counter++], DNATools.getDNA());
>>> }
>>> }
>>>
>>> You can then instantiate an object using MyDNASeqIterator's
>>> constructor to give it your string array, and iterate over it to get
>>> corresponding RichSequence instances.
>>>
>>> To convert your sequences to FASTA, use the above iterator to
>>> generate sequences to pass to FastaFormat in the same way that you
>>> would write a normal FASTA file.
>>>
>>> cheers,
>>> Richard
>>>
>>> On 6 Dec 2009, at 14:04, Oliver Stolpe wrote:
>>>
>>>
>>>> Hello *,
>>>>
>>>> I have a set of sequences as strings in an array. I now want to
>>>> turn them into an iterator over RichSequences in fasta-format. I
>>>> read in the cookbook, but I dont get it. And looked up the examples
>>>> in biojavax-doc. I tried much but I have no good starting point. No
>>>> starting point at all. How do the RichSequenceBuilder work? What
>>>> about the FastaFormat-thing?
>>>> I thought about putting the sequences in a fast-file and then read
>>>> the file. But there must be a much more straight-forward way!
>>>>
>>>> Thanks in advance for any hints,
>>>> Oliver
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>> --
>> 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/
>>
>>
>
>
> Mit den besten Grüßen,
> Oliver
>
>
> ------------------------------------------------------------------------
>
> Subject:
> Re: [Biojava-l] A Exception Has Occurred During Parsing.
> From:
> ilhami visne <ilhami.visne at gmail.com>
> Date:
> Fri, 11 Dec 2009 12:36:46 +0100
> To:
> Richard Holland <holland at eaglegenomics.com>
>
> To:
> Richard Holland <holland at eaglegenomics.com>
> CC:
> biojava-l at lists.open-bio.org
>
>
> 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/
>>
>>
>>
>
>
>
> ------------------------------------------------------------------------
>
> Subject:
> Re: [Biojava-l] A Exception Has Occurred During Parsing.
> From:
> Richard Holland <holland at eaglegenomics.com>
> Date:
> Fri, 11 Dec 2009 14:17:21 +0000
> To:
> ilhami visne <ilhami.visne at gmail.com>
>
> To:
> ilhami visne <ilhami.visne at gmail.com>
> CC:
> biojava-l at lists.open-bio.org
>
>
> If the problem is random, it's almost certainly due to problems with the NCBI server feeding you data. There are restrictions on usage - e.g. NCBI only allows a certain number of requests - so you might be running into those.
>
> cheers,
> Richard
>
> On 11 Dec 2009, at 11:36, ilhami visne wrote:
>
>
>> 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/
>>>
>>>
>>>
>>>
>>>
>>>
>
> --
> 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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