[Bioperl-l] getting the Sbjct database from a hit

[Hilmar Lapp]

Catherine Letondal wrote:
> 
> Hilmar Lapp writes:
> > First, usually you don't create Sbjct objects yourself, but obtain them
> > from a Bio::Tools::Blast object created from a BLAST report. As you're
> > writing this first, I assume that's in fact what you're doing.
> >
> > I'm not sure what you're referring to with the database() method. If you
> > want to get the name of the database the sequence was searched against,
> > you can simply call $blast->database().
> 
> Actually I need the database of the subject - since the searched database may be
> a non-redundant database containing entries from pir or swissprot :
> [...]
> sp|P02914|MALK_ECOLI MALTOSE/MALTODEXTRIN TRANSPORT ATP-BINDING ...   738  0.0
> pir||MMECMK inner membrane protein malK - Escherichia coli >gi|4...   734  0.0
> sp|P19566|MALK_SALTY MALTOSE/MALTODEXTRIN TRANSPORT ATP-BINDING ...   696  0.0
> pir||S05329 inner membrane protein malK - Salmonella typhimurium      689  0.0
> [...]
> 
> > To obtain the database containing
> > the hit (i.e., the database part of the identifier for those cases in
> > which the identifier is a compound of database and accession) you have to
> > interpret $hit->name() yourself, as the documentation tells.
> > $hit->database() will only return a dash ('-').
> 
> That's right! But the name $hit->name() does *not* return the database in it:
> 
> For example, for the hit:
> 
>         sp|Q00752|MSMK_STRMU MULTIPLE SUGAR-BINDING TRANSPORT ATP-BINDI...   298  2e-81
> 
> This statement:
>         print STDERR "hit name: ",$hit->name,"\n";
> prints:
>         hit name: Q00752/MSMK_STRMU
> The 'sp' has disappeared...
> 
> --
> Catherine Letondal -- Pasteur Institute Computing Center

I'd consider this a bug (BTW is '/' instead of the original '|' a typo of
yours? Otherwise it's a bug, too). Could you please submit your response
(for detailing the problem) along with the Blast report or the sequence
(if it's plain NCBI Blast output against one of their databanks, and if
so, please indicate which) to bioperl-bugs@bio.perl.org.

	Hilmar

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Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
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