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benn | 4 Jun 2008 11:56
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GFF Parsing

Hello,

          I am investigating the user of biojava for file parsing for 
in-house apps in my organisation.  I have previously used biojava but if 
I am looking at a new implementation then I would like to use biojavax.  
I have managed to parse a fasta file with no problems but I now need to 
parse gff.  I cannot see a parser for gff in biojavax, would I need to 
implement a new parser which works with the biojavax IOTools and rich 
sequence or can I use the parser from biojava2 in some way?

Cheers,

Neil
_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> lists.open-bio.org
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Richard Holland | 4 Jun 2008 21:34
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Re: GFF Parsing

Hello. BioJavaX has no GFF parser yet, but we would most certainly
welcome one. It'd have to be a from-scratch parser although you could
certainly use the BJ2 parser as reference for working out what to put
where in the object model. The idea of the BJX parsers was to make
better use of the object model than the BJ2 ones, so you might have to
move a few things to more appropriate slots.

Also, take a look on the BioJava website about our discussions for
BioJava 3 - on which work will start shortly.

Thanks for your interest!

cheers,
Richard

2008/6/4 benn <benn <at> mpi-cbg.de>:
> Hello,
>
>         I am investigating the user of biojava for file parsing for in-house
> apps in my organisation.  I have previously used biojava but if I am looking
> at a new implementation then I would like to use biojavax.  I have managed
> to parse a fasta file with no problems but I now need to parse gff.  I
> cannot see a parser for gff in biojavax, would I need to implement a new
> parser which works with the biojavax IOTools and rich sequence or can I use
> the parser from biojava2 in some way?
>
> Cheers,
>
> Neil
> _______________________________________________
(Continue reading)

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Allan Kamau | 5 Jun 2008 13:10
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Simple sequence viewer (may be off topic)

Hi all,
Am looking for a simple sequence viewer to install on a Linux 
workstation. This tool should allow viewing and editing of alignments, 
any suggestions.
I've googled without much success. Did not know where else to ask.

Allan.
_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> lists.open-bio.org
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benn | 5 Jun 2008 13:49
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Problem while using BlastXMLParserFacade

Hello,

        Sorry to pepper the board with questions!  I am working on BLAST 
parsing and have the standard output for BLAST working fine with JUnit 
tests.  So I am attempting to recreate this for files in XML format 
coming from blast (blastp), however I have the problem that I get a 
SAXException that content is not allowed before prolog.  I thought I 
could have some invisible characters which is causing it to throw a 
wobbly but I cannot see any.  Has anyone else come across the problem?  
For completeness, the file can be downloaded at : 
http://idisk-srv1.mpi-cbg.de/~benn/xmloutput.xml (the mailing list 
server would not me attach the file to the email) and the code which 
parses is below:

<code>
  private List<SeqSimilaritySearchResult> parseBlast(String filename)
          throws IOException, SAXException, BioException {

      InputStream is = new FileInputStream(
              "src/test/resources/blast/standardoutput.blastp");

      BlastXMLParserFacade parser = new BlastXMLParserFacade();
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
      parser.setContentHandler(adapter);
      List<SeqSimilaritySearchResult> results = new 
ArrayList<SeqSimilaritySearchResult>();

      SearchContentHandler builder = new BlastLikeSearchBuilder(results,
              new DummySequenceDB("queries"),
              new DummySequenceDBInstallation());
(Continue reading)

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Andreas Prlic | 5 Jun 2008 13:52
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Re: Simple sequence viewer (may be off topic)

HI Allan,

The best alignment viewer and editor in my opinion is Jalview http:// 
www.jalview.org/

Andreas

On 5 Jun 2008, at 12:10, Allan Kamau wrote:

> Hi all,
> Am looking for a simple sequence viewer to install on a Linux  
> workstation. This tool should allow viewing and editing of  
> alignments, any suggestions.
> I've googled without much success. Did not know where else to ask.
>
> Allan.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
                               +44 (0) 1223 49 6891

-----------------------------------------------------------------------

--

-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research
(Continue reading)

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Felix Dreher | 5 Jun 2008 14:08
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Re: Simple sequence viewer (may be off topic)

Hi Allan,

you could try the Argo genome browser:
        --> http://www.broad.mit.edu/annotation/argo/

Regards,
Felix

Allan Kamau wrote:
> Hi all,
> Am looking for a simple sequence viewer to install on a Linux 
> workstation. This tool should allow viewing and editing of alignments, 
> any suggestions.
> I've googled without much success. Did not know where else to ask.
>
> Allan.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--

-- 
 ______________________________________________

 Felix Dreher
 Max Planck Institute for Molecular Genetics
 Department of Vertebrate Genomics
 Bioinformatics Group

 Ihnestr. 73     |  phone: 0049-30-84131279
 D-14195 Berlin  |  mobile: 0049-163-7542426
(Continue reading)

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Gabrielle Doan | 5 Jun 2008 15:32
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features of a sequence

Hi all,

I would like to query the features of a sequence with following code:

<code>
public class Test{
      public static void main(String[] args) {
        // load Hibernate config

        SessionFactory sessionFactory = new 
Configuration().configure().buildSessionFactory();        // open the 
session
        Session session = sessionFactory.openSession();
        // connect it to BioJavaX
        RichObjectFactory.connectToBioSQL(session);

        Transaction tx = session.beginTransaction();
              Query q1 = session.createQuery(
                "from Feature as f " +
                "inner join fetch f.noteSet as n " +
                "where n.value=:val and f.typeTerm.name=:term");
        q1.setString("val","TRNF");
        q1.setString("term","gene"); 
List<SimpleRichFeature> li = q1.list(); 
System.out.println("Found:\t"+li.size());
        for (Iterator<SimpleRichFeature> i = li.iterator(); i.hasNext(); ){
            SimpleRichFeature f = i.next();
            System.out.println("Term:\t"+f.getTypeTerm().getName());

System.out.println("Location:\t"+f.getLocation().getMin()+"\t"+f.getLocation().getMax());
(Continue reading)

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Richard Holland | 5 Jun 2008 18:25
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Re: features of a sequence

Oh dear, you found a bug.....! This is occurring in the location
flattening routines in RichLocation.Tools, where it is inadvertently
overwriting location data collection objects that should have been
just emptied and repopulated instead of being replaced.

I'll try and fix this. Can't promise it soon - I'm away for the next 7
days and am a bit busy after that - but will make a note. Maybe
someone else here could fix it quicker? (please?! :) )

cheers,
Richard

2008/6/5 Gabrielle Doan <gabrielle_doan <at> gmx.net>:
> Hi all,
>
> I would like to query the features of a sequence with following code:
>
> <code>
> public class Test{
>     public static void main(String[] args) {
>       // load Hibernate config
>
>       SessionFactory sessionFactory = new
> Configuration().configure().buildSessionFactory();        // open the
> session
>       Session session = sessionFactory.openSession();
>       // connect it to BioJavaX
>       RichObjectFactory.connectToBioSQL(session);
>
>       Transaction tx = session.beginTransaction();
(Continue reading)

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Mark Schreiber | 6 Jun 2008 04:34
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Re: Problem while using BlastXMLParserFacade

Hi -

I have seen this problem twice. Once it was due to 'invisible' white
space before the XML. If you call trim() on the String that you get
from the file you can get rid of this. You may not even be able to see
it as some meta-characters are non-printing.  The other problem is if
your file was produced and saved on linux/unix and parsed on Windows.
Problems can occur due to the different line feeds and carriage
returns. While Java automatically knows which combination works for
which operating it will assume the file you are working on came from
your operating system.  If this is the problem you can solve it using
the unix utility dos2unix or unix2dos depending on which way you are
going.

- Mark

On Thu, Jun 5, 2008 at 7:49 PM, benn <benn <at> mpi-cbg.de> wrote:
>
> Hello,
>
>       Sorry to pepper the board with questions!  I am working on BLAST parsing and have the standard output for
BLAST working fine with JUnit tests.  So I am attempting to recreate this for files in XML format coming from
blast (blastp), however I have the problem that I get a SAXException that content is not allowed before
prolog.  I thought I could have some invisible characters which is causing it to throw a wobbly but I cannot
see any.  Has anyone else come across the problem?  For completeness, the file can be downloaded at :
http://idisk-srv1.mpi-cbg.de/~benn/xmloutput.xml (the mailing list server would not me attach the
file to the email) and the code which parses is below:
>
> <code>
>  private List<SeqSimilaritySearchResult> parseBlast(String filename)
(Continue reading)

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Mark Schreiber | 6 Jun 2008 04:39
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Re: features of a sequence

Can someone post a bug report for this just to make sure it gets
logged and fixed at some point?

Thanks,

- Mark

On Fri, Jun 6, 2008 at 12:25 AM, Richard Holland
<dicknetherlands <at> gmail.com> wrote:
> Oh dear, you found a bug.....! This is occurring in the location
> flattening routines in RichLocation.Tools, where it is inadvertently
> overwriting location data collection objects that should have been
> just emptied and repopulated instead of being replaced.
>
> I'll try and fix this. Can't promise it soon - I'm away for the next 7
> days and am a bit busy after that - but will make a note. Maybe
> someone else here could fix it quicker? (please?! :) )
>
> cheers,
> Richard
>
> 2008/6/5 Gabrielle Doan <gabrielle_doan <at> gmx.net>:
>> Hi all,
>>
>> I would like to query the features of a sequence with following code:
>>
>> <code>
>> public class Test{
>>     public static void main(String[] args) {
>>       // load Hibernate config
(Continue reading)

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Gmane