[Bioperl-l] accessing EMBL database

Mark A. Jensen maj at fortinbras.us
Thu Nov 19 09:17:05 EST 2009

I'm inclined to agree. Lots of responses to questions here that begin
"Well, as the error message said, you need to check...", which means
people tend towards "I broke it! Write the list!". I do find it hairy when
my errors are way down in the object tree.
----- Original Message ----- 
From: "Dave Messina" <David.Messina at sbc.su.se>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <bioperl-l at bioperl.org>
Sent: Thursday, November 19, 2009 9:04 AM
Subject: Re: [Bioperl-l] accessing EMBL database

> 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 

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: 
STACK: trial2.pl

Just a thought. This has probably been discussed before.

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