[Biojava-dev] bioperl like blastparser

[Richard Holland]

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Definitely, yes! Thanks!

Andreas Prlic (copied on this) will be able to help you more as he
already knows a lot about the existing parser.

cheers,
Richard

Michael Gang wrote:
> Hi All,
> 
> I used the interface of the java blast parser.
> I had mainly two problems with it:
> 1) The blast parser does not parse all the information (for example
> query length)
> 2) The blast parser parses the whole blast report into a list which
> eats a lot of memory.
> 
> I would be interested to write and contribute a blast parser which
> parses all the information of the blast and parses the blast
> iteratively.
> Something like the following code in bioperl (just in Java).
>   use Bio::SearchIO;
>     # format can be 'fasta', 'blast'
>     my $searchio = new Bio::SearchIO( -format => 'blastxml',
>                                       -file   => 'blastout.xml' );
>     while ( my $result = $searchio->next_result() ) {
>        while( my $hit = $result->next_hit ) {
>         # process the Bio::Search::Hit::HitI object
>            while( my $hsp = $hit->next_hsp ) {
>             # process the Bio::Search::HSP::HSPI object
>         }
>     }
> 
> Would you be interested in such a contribution ?
> 
> Best regards,
> Michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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