[Bioperl-l] accessing EMBL database

Dave Messina David.Messina at sbc.su.se
Thu Nov 19 09:04:55 EST 2009

> I would agree that the error message is not really informative.

Agreed that it could be better, but I wonder whether part of the problem with BioPerl error messages is the stack dump.

I think a lot of eyes just glaze right over when they see a big wad of complicated stuff, with colons and slashes and line numbers, spewing out at them.

Perhaps the stack dump should be turned off by default?

Wouldn't this:

ERROR: EMBL stream with no ID. Not embl in my book

Be a lot clearer than this?:

MSG: EMBL stream with no ID. Not embl in my book
STACK: Error::throw
STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm: 368
STACK: Bio::SeqIO::embl::next_seq C:/Perl/site/lib/Bio\SeqIO\embl.pm: 203
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm: 194
STACK: trial2.pl

Just a thought. This has probably been discussed before.

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