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

Catherine Letondal letondal@pasteur.fr
Sun, 08 Oct 2000 15:23:00 +0200

"Stephen A. Chervitz" writes:
> Catherine,
> You've discovered a recent change in the Blast Sbjct object regarding the handling of hit
> identifiers. The Sbjct no longer assumes any structure in the hit identifier. It simply
> takes the first non-whitespace containing chunk of text from the hit description line and
> assignes it to the name of the hit. You then need to parse the $hit->name to extract the
> database yourself now.
> The behavior you described below, of hit name containing something like
> "Q00752/MSMK_STRMU", is from the former version of Sbjct which stripped out database name
> and concatenated identifiers with a '/' separator. The new version will produce a string
> such as "sp|Q00752|MSMK_STRMU" and $hit->database will be '-', as Hilmar said. (The
> database method is unofficially deprecated - we should make this official.)

As I already said to Hilmar, the the name returned by $hit->name()  does *not* return 
the database in it (version 0.6.1):

> > For example, for the hit:
> >
> >
> > 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