[Biojava-l] Parse a Blast

[Sébastien PETIT]

Hello, Mark

Thanks for the answer...
The parser you talked me about, may be the good one...
But I'm maybe not enought good in Java and I can't use it.
I spent all the morning trying to understand this class and how it
works, but, nothing....I didn't understand how I can use it...

Thank you for any additional help

Great-Fred


--- mark.schreiber at novartis.com a écrit :

> Hello -
> 
> I suspect the problem is that you are using the BlastLikeSAXParser.
> This 
> was written in the days before blast xml was available (and stable)
> and is 
> an adapter that parses a non-xml blast report and produces SAX
> events.
> 
> The parser you want is
> org.biojava.bio.program.sax.blastxml.BlastXMLParser
> 
> Hope this helps,
> 
> - Mark
> 
> 
> 
> 
> Sébastien PETIT <great_fred at yahoo.com>
> Sent by: biojava-l-bounces at portal.open-bio.org
> 06/10/2005 10:18 PM
> 
>  
>         To:     biojava-l at biojava.org
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] Parse a Blast
> 
> 
> Hello
> 
> First of all, sorry for my English (I'm French..)
> Now, my problem...
> I have Blast in XML format. I want to parse it because I want just
> the
> alignment.
> But, when I use a script found on the Net, the answer is :
> --> org.xml.sax.SAXException: Could not recognise the format of this
> file as one supported by the framework.
> 
> Does anybody have the same problem?
> Or Does anybody have an idea to resolve my problem?
> 
> Here is the script (Sorry, the comment are in French..)
> 
>    import java.io.*;
>    import java.util.*;
> 
>    import org.biojava.bio.program.sax.*;
>    import org.biojava.bio.program.ssbind.*;
>    import org.biojava.bio.search.*;
>    import org.biojava.bio.seq.db.*;
>    import org.xml.sax.*;
>    import org.biojava.bio.*;
> 
>     public class BlastParser {
>    /**
>    * args[0] est assumé être le nom du fichier de sortie BLAST */
>        public static void main(String[] args) {
>          try {
>          //obtenir les entrées Blast sous la forme de Stream
>             InputStream is = new FileInputStream(args[0]);
>  
>          //construire un BlastLikeSAXParser
>             BlastLikeSAXParser parser = new BlastLikeSAXParser();
>  
>          //construire un adaptateur pour SAX event qui les passera a
> un
> Handler.
>             SeqSimilarityAdapter adapter = new
> SeqSimilarityAdapter();
>  
>          //initialiser l'adaptateur des SAX events  de l'objet parser
>             parser.setContentHandler(adapter);
>  
>          //la liste qui contiendra les SeqSimilaritySearchResults
>             List results = new ArrayList();
>  
>          //créer le SearchContentHandler qui construira les
> SeqSimilaritySearchResults
>          //dans la liste results
>             SearchContentHandler builder = new
> BlastLikeSearchBuilder(results,
>                new DummySequenceDB("queries"), new
> DummySequenceDBInstallation());
>  
>          //enregistrer builder aupres de adapter
>             adapter.setSearchContentHandler(builder);
>  
>          //parcourir le fichier; après, la liste result contiendra
>          //les SeqSimilaritySearchResults
>  
>             parser.parse(new InputSource(is));
>             //formatResults(results);
>          }
>              catch (SAXException ex) {
>             //probleme de XML
>                ex.printStackTrace();
>             }
>              catch (IOException ex) {
>             //probleme de IO, comme un fichier introuvable
>                ex.printStackTrace();
>             }
>       }
>    }
> 
> Thank you for any answer...
> 
> Great-Fred
> 
> 
>  
> 
>  
>  
>
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> 
> 



	

	
		
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