[Bioperl-l] Bio::DB:: queries

[Jason Stajich]

The differences in your code would be:

foreach my $acc ( @acc ) {
  eval {
   $seq = $db->get_Seq_by_acc($acc);
  };
  if( $@) {
    print STDERR "skipping $acc, it could not be found\n";
    next;
  }

}

OR

foreach my $acc ( @acc ) {
  my $seq = $db->get_Seq_by_acc($acc);
  if( ! $seq ) {
   print STDERR "skipping $acc, it could not be found\n";
   next;
  }
}


If you call get_Stream_by_acc([@listofaccs]) I don't think it will
currently throw an exception, just if the entire query fails.

-jason
On Tue, 10 Jun 2003, Prachi Shah wrote:

> I would be happier if warnings were sent out instead
> of exceptions. If we are using a large accession list,
> it is quite likely that there will be atleast some
> accessions which may belong to some other database or
> something like it.
>
> Prachi.
>
>
> --- Jason Stajich <jason at cgt.duhs.duke.edu> wrote:
> > Does it make sense for us to be throwing exceptions
> > when an accession or
> > id is not found in a db search (i.e.
> > Bio::DB::GenBank) or give a warning
> > (which can be silenced with -verbose => -1) and
> > return undef?
> >
> > Do people have a strong feeling one way or another
> > here?
> > -jason
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> >
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu