[Bioperl-l] Bio::SearchIO $hit->description(), only one line returned...

[Jason Stajich]

It's a bug in 1.0.2 for blast parsing which has been since fixed on the
main trunk - bioperl dev release 1.1.1 has the fix as will
soon-to-be-out 1.2

http://bugzilla.bioperl.org/show_bug.cgi?id=1193


Ewan - perhaps a preview release of 1.2 should be bundled up?

-jason
On Tue, 17 Dec 2002, Martin Schenker wrote:

> Hi all,
>
> this might be a daft question, but I spend some time searching the web & the
> BioPerl 1.0.2 documentation and couldn't find a hint.
>
> I'm trying to retrieve BLAST hit descriptions which span several lines in
> the BLAST output. Up to now I only can get the first line. Anything I'm
> missing here?
>
> ========================================================
>
> BLASTP 2.2.4 [Aug-26-2002]
>
> Query= test1|
>          (668 letters)
>
> Database: /data/scratch/db/ENSEMBL_9.30_pep
>            27,628 sequences; 12,353,235 total letters
>
> Searching..................................................done
>
>
> Score    E
> Sequences producing significant alignments:                      (bits)
> Value
>
> ENSP00000264758 (ALPHA ADDUCIN (ERYTHROCYTE ADDUCIN ALPHA SUBUNI...  1178
> 0.0
>
> >ENSP00000264758 (ALPHA ADDUCIN (ERYTHROCYTE ADDUCIN ALPHA SUBUNIT).
>            [Source:SWISSPROT;Acc:P35611]) Clone:Z68280
>            Contig:Z68280.1.1.43583 Chr:4 Basepair:2834529
>            Status:known
>           Length = 631
> ============================================================================
> ======
>
> If I use Bio::SearchIO and call
>
> my $descr = $hit->description();
>
> I only can retrieve the first line:
>
> "(ALPHA ADDUCIN (ERYTHROCYTE ADDUCIN ALPHA SUBUNIT)."
>
> Is there any way to get the full description back up to the "Length = 631"
> statement, like
>
> "(ALPHA ADDUCIN (ERYTHROCYTE ADDUCIN ALPHA SUBUNIT).
> [Source:SWISSPROT;Acc:P35611]) Clone:Z68280 Contig:Z68280.1.1.43583 Chr:4
> Basepair:2834529 Status:known"
>
> ?
>
> Cheers for any pointers...
>
> Martin
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu